151
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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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152
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Zeng X, Guo Y, Xu Q, Mascher M, Guo G, Li S, Mao L, Liu Q, Xia Z, Zhou J, Yuan H, Tai S, Wang Y, Wei Z, Song L, Zha S, Li S, Tang Y, Bai L, Zhuang Z, He W, Zhao S, Fang X, Gao Q, Yin Y, Wang J, Yang H, Zhang J, Henry RJ, Stein N, Tashi N. Origin and evolution of qingke barley in Tibet. Nat Commun 2018; 9:5433. [PMID: 30575759 PMCID: PMC6303313 DOI: 10.1038/s41467-018-07920-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 12/05/2018] [Indexed: 11/09/2022] Open
Abstract
Tibetan barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on the Tibetan Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based on deep-coverage whole-genome and published exome-capture resequencing data for a total of 437 accessions, we show that contemporary qingke is derived from eastern domesticated barley and it is introduced to southern Tibet most likely via north Pakistan, India, and Nepal between 4,500 and 3,500 years ago. The low genetic diversity of qingke suggests Tibet can be excluded as a center of origin or domestication for barley. The rapid decrease in genetic diversity from eastern domesticated barley to qingke can be explained by a founder effect from 4,500 to 2,000 years ago. The haplotypes of the five key domestication genes of barley support a feral or hybridization origin for Tibetan weedy barley and reject the hypothesis of native Tibetan wild barley.
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Affiliation(s)
- Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Yu Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qijun Xu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, 999077, China
| | - Likai Mao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Qingfeng Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhanfeng Xia
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Juhong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Hongjun Yuan
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | | | - Yulin Wang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Zexiu Wei
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Li Song
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Sang Zha
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Shiming Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yawei Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China
- Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China
| | - Lijun Bai
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, 610041, China
| | - Zhenhua Zhuang
- Chengdu Life Baseline Technology Co., Ltd., Chengdu, 610041, China
| | - Weiming He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ye Yin
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou, 310058, China
| | - Jing Zhang
- Institute of Crop Science, Chinese Academy of Agriculture Sciences, Beijing, 100081, China
| | - Robert J Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany.
| | - Nyima Tashi
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa, 850002, China.
- Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa Tibet, 850002, China.
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153
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Wallace JG, Rodgers-Melnick E, Buckler ES. On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics. Annu Rev Genet 2018; 52:421-444. [DOI: 10.1146/annurev-genet-120116-024846] [Citation(s) in RCA: 111] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Understanding the quantitative genetics of crops has been and will continue to be central to maintaining and improving global food security. We outline four stages that plant breeding either has already achieved or will probably soon achieve. Top-of-the-line breeding programs are currently in Breeding 3.0, where inexpensive, genome-wide data coupled with powerful algorithms allow us to start breeding on predicted instead of measured phenotypes. We focus on three major questions that must be answered to move from current Breeding 3.0 practices to Breeding 4.0: ( a) How do we adapt crops to better fit agricultural environments? ( b) What is the nature of the diversity upon which breeding can act? ( c) How do we deal with deleterious variants? Answering these questions and then translating them to actual gains for farmers will be a significant part of achieving global food security in the twenty-first century.
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Affiliation(s)
- Jason G. Wallace
- Department of Crop and Soil Sciences, The University of Georgia, Athens, Georgia 30602, USA
| | | | - Edward S. Buckler
- United States Department of Agriculture, Agricultural Research Service, Ithaca, New York 14853, USA
- Institute for Genomic Diversity, Cornell University, Ithaca, New York 14853, USA
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154
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Milner SG, Jost M, Taketa S, Mazón ER, Himmelbach A, Oppermann M, Weise S, Knüpffer H, Basterrechea M, König P, Schüler D, Sharma R, Pasam RK, Rutten T, Guo G, Xu D, Zhang J, Herren G, Müller T, Krattinger SG, Keller B, Jiang Y, González MY, Zhao Y, Habekuß A, Färber S, Ordon F, Lange M, Börner A, Graner A, Reif JC, Scholz U, Mascher M, Stein N. Genebank genomics highlights the diversity of a global barley collection. Nat Genet 2018; 51:319-326. [PMID: 30420647 DOI: 10.1038/s41588-018-0266-x] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/26/2018] [Indexed: 01/22/2023]
Abstract
Genebanks hold comprehensive collections of cultivars, landraces and crop wild relatives of all major food crops, but their detailed characterization has so far been limited to sparse core sets. The analysis of genome-wide genotyping-by-sequencing data for almost all barley accessions of the German ex situ genebank provides insights into the global population structure of domesticated barley and points out redundancies and coverage gaps in one of the world's major genebanks. Our large sample size and dense marker data afford great power for genome-wide association scans. We detect known and novel loci underlying morphological traits differentiating barley genepools, find evidence for convergent selection for barbless awns in barley and rice and show that a major-effect resistance locus conferring resistance to bymovirus infection has been favored by traditional farmers. This study outlines future directions for genomics-assisted genebank management and the utilization of germplasm collections for linking natural variation to human selection during crop evolution.
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Affiliation(s)
- Sara G Milner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Matthias Jost
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Agriculture and Food, The Commonwealth Scientific and Industrial Research Organisation, Canberra, Australia
| | - Shin Taketa
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Elena Rey Mazón
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Markus Oppermann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Stephan Weise
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martín Basterrechea
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Patrick König
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Danuta Schüler
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Rajiv Sharma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,University of Dundee at the James Hutton Institute, Invergowrie, UK
| | - Raj K Pasam
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,Department of Economic Development, Jobs, Transport and Resources, Centre for AgriBioscience, Agriculture Victoria Research, Bundoora, Victoria, Australia
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Ganggang Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Dongdong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Gerhard Herren
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.,Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Maria Y González
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Antje Habekuß
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Sandra Färber
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute (Federal Research Centre for Cultivated Plants), Quedlinburg, Germany
| | - Matthias Lange
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany. .,Center for Integrated Breeding Research, Georg-August-Universität Göttingen, Göttingen, Germany.
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155
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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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156
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Case AJ, Bhavani S, Macharia G, Pretorius Z, Coetzee V, Kloppers F, Tyagi P, Brown-Guedira G, Steffenson BJ. Mapping adult plant stem rust resistance in barley accessions Hietpas-5 and GAW-79. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:2245-2266. [PMID: 30109391 DOI: 10.1007/s00122-018-3149-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/23/2018] [Indexed: 06/08/2023]
Abstract
Key message Major stem rust resistance QTLs proposed to be Rpg2 from Hietpas-5 and Rpg3 from GAW-79 were identified in chromosomes 2H and 5H, respectively, and will enhance the diversity of stem rust resistance in barley improvement programs. Stem rust is a devastating disease of cereal crops worldwide. In barley (Hordeum vulgare ssp. vulgare), the disease is caused by two pathogens: Puccinia graminis f. sp. secalis (Pgs) and Puccinia graminis f. sp. tritici (Pgt). In North America, the stem rust resistance gene Rpg1 has protected barley from serious losses for more than 60 years; however, widely virulent Pgt races from Africa in the Ug99 group threaten the crop. The accessions Hietpas-5 (CIho 7124) and GAW-79 (PI 382313) both possess moderate-to-high levels of adult plant resistance to stem rust and are the sources of the resistance genes Rpg2 and Rpg3, respectively. To identify quantitative trait loci (QTL) for stem rust resistance in Hietpas-5 and GAW-79, two biparental populations were developed with Hiproly (PI 60693), a stem rust-susceptible accession. Both populations were phenotyped to the North American Pgt races of MCCFC, QCCJB, and HKHJC in St. Paul, Minnesota, and to African Pgt races (predominately TTKSK in the Ug99 group) in Njoro, Kenya. In the Hietpas-5/Hiproly population, a major effect QTL was identified in chromosome 2H, which is proposed as the location for Rpg2. In the GAW-79/Hiproly population, a major effect QTL was identified in chromosome 5H and is the proposed location for Rpg3. These QTLs will enhance the diversity of stem rust resistance in barley improvement programs.
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Affiliation(s)
- Austin J Case
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Sridhar Bhavani
- Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT), Nairobi, Kenya
| | - Godwin Macharia
- Kenya Agriculture and Livestock Research Organization (KALRO), Njoro, Kenya
| | - Zacharias Pretorius
- Department of Plant Sciences, University of the Free State, Bloemfontein, Republic of South Africa
| | - Vicky Coetzee
- Pannar Seed (Pyt) Ltd, Greytown, Republic of South Africa
| | | | - Priyanka Tyagi
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | | | - Brian J Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA.
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157
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Huang Y, Haas M, Heinen S, Steffenson BJ, Smith KP, Muehlbauer GJ. QTL Mapping of Fusarium Head Blight and Correlated Agromorphological Traits in an Elite Barley Cultivar Rasmusson. FRONTIERS IN PLANT SCIENCE 2018; 9:1260. [PMID: 30233612 PMCID: PMC6127635 DOI: 10.3389/fpls.2018.01260] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/09/2018] [Indexed: 05/05/2023]
Abstract
Fusarium head blight (FHB) is an important fungal disease affecting the yield and quality of barley and other small grains. Developing and deploying resistant barley cultivars is an essential component of an integrated strategy for reducing the adverse effects of FHB. Genetic mapping studies have revealed that resistance to FHB and the accumulation of pathogen-produced mycotoxins are controlled by many quantitative trait loci (QTL) with minor effects and are highly influenced by plant morphological traits and environmental conditions. Some prior studies aimed at mapping FHB resistance have used populations derived from crossing a Swiss landrace Chevron with elite breeding lines/cultivars. Both Chevron and Peatland, a sib-line of Chevron, were used as founders in the University of Minnesota barley breeding program. To understand the native resistance that might be present in the Minnesota breeding materials, a cross of an elite cultivar with a susceptible unadapted genotype is required. Here, a mapping population of 93 recombinant inbred lines (RILs) was developed from a cross between a moderately susceptible elite cultivar 'Rasmusson' and a highly susceptible Japanese landrace PI 383933. This population was evaluated for FHB severity, deoxynivalenol (DON) accumulation and various agromorphological traits. Genotyping of the population was performed with the barley iSelect 9K SNP chip and 1,394 SNPs were used to develop a genetic map. FHB severity and DON accumulation were negatively correlated with plant height (HT) and spike length (SL), and positively correlated with spike density (SD). QTL analysis using composite interval mapping (CIM) identified the largest effect QTL associated with FHB and DON on the centromeric region of chromosome 7H, which was also associated with HT, SL, and SD. A minor FHB QTL and a minor DON QTL were detected on chromosome 6H and chromosome 3H, respectively, and the Rasmusson alleles contributed to resistance. The 3H DON QTL likely represents native resistance in elite germplasm as the marker haplotype of Rasmusson at this QTL is distinct from that of Chevron. This study highlights the relationship between FHB resistance/susceptibility and morphological traits and the need for breeders to account for morphology when developing FHB resistant genotypes.
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Affiliation(s)
- Yadong Huang
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Matthew Haas
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Shane Heinen
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Brian J. Steffenson
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, United States
| | - Kevin P. Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, United States
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158
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Anwar N, Ohta M, Yazawa T, Sato Y, Li C, Tagiri A, Sakuma M, Nussbaumer T, Bregitzer P, Pourkheirandish M, Wu J, Komatsuda T. miR172 downregulates the translation of cleistogamy 1 in barley. ANNALS OF BOTANY 2018; 122:251-265. [PMID: 29790929 PMCID: PMC6070043 DOI: 10.1093/aob/mcy058] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 04/30/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND AND AIMS Floret opening in barley is induced by the swelling of the lodicule, a trait under the control of the cleistogamy1 (cly1) gene. The product of cly1 is a member of the APETALA2 (AP2) transcription factor family, which inhibits lodicule development. A sequence polymorphism at the miR172 target site within cly1 has been associated with variation in lodicule development and hence with the cleistogamous phenotype. It was unclear whether miR172 actually functions in cly1 regulation and, if it does, which miR172 gene contributes to cleistogamy. It was also interesting to explore whether miR172-mediated cly1 regulation occurs at transcriptional level or at translational level. METHODS Deep sequencing of small RNA identified the miR172 sequences expressed in barley immature spikes. miR172 genes were confirmed by computational and expression analysis. miR172 and cly1 expression profiles were determined by in situ hybridization and quantitative expression analysis. Immunoblot analysis provided the CLY1 protein quantifications. Definitive evidence of the role of miR172 in cleistogamy was provided by a transposon Ds-induced mutant of Hv-miR172a. KEY RESULTS A small RNA analysis of the immature barley spike revealed three isomers, miR172a, b and c, of which miR172a was the most abundant. In situ hybridization analysis showed that miR172 and cly1 co-localize in the lodicule primordium, suggesting that these two molecules potentially interact with one another. Immunoblot analysis showed that the sequence polymorphism at the miR172 target site within cly1 reduced the abundance of the CLY1 protein, but not that of its transcript. In a Ds-induced mutant of Hv-miR172a, which generates no mature miR172a, the lodicules fail to grow, resulting in a very small lodicule. CONCLUSIONS Direct evidence is presented to show that miR172a acts to reduce the abundance of the CLY1 protein, which enables open flowering in barley.
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Affiliation(s)
- Nadia Anwar
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Masaru Ohta
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Takayuki Yazawa
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Yutaka Sato
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Chao Li
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Mari Sakuma
- National Institute of Agrobiological Sciences, Tsukuba, Japan
| | - Thomas Nussbaumer
- Munich Information Center for Protein Sequences, Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, Neuherberg, Germany
- Division of Computational System Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Phil Bregitzer
- USDA-ARS, National Small Grains Germplasm Research Facility, Aberdeen, ID, USA
| | - Mohammad Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- The University of Sydney, Faculty of Agriculture and Environment, Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan
- National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- For correspondence. E-mail
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Shao J, Haider I, Xiong L, Zhu X, Hussain RMF, Övernäs E, Meijer AH, Zhang G, Wang M, Bouwmeester HJ, Ouwerkerk PBF. Functional analysis of the HD-Zip transcription factor genes Oshox12 and Oshox14 in rice. PLoS One 2018; 13:e0199248. [PMID: 30028850 PMCID: PMC6054374 DOI: 10.1371/journal.pone.0199248] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/04/2018] [Indexed: 12/19/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factor family plays vital roles in plant development and morphogenesis as well as responses to biotic and abiotic stresses. In barley, a recessive mutation in Vrs1 (HvHox1) changes two-rowed barley to six-rowed barley, which improves yield considerably. The Vrs1 gene encodes an HD-Zip subfamily I transcription factor. Phylogenetic analysis has shown that the rice HD-Zip I genes Oshox12 and Oshox14 are the closest homologues of Vrs1. Here, we show that Oshox12 and Oshox14 are ubiquitously expressed with higher levels in developing panicles. Trans-activation assays in yeast and rice protoplasts demonstrated that Oshox12 and Oshox14 can bind to a specific DNA sequence, AH1 (CAAT(A/T)ATTG), and activate reporter gene expression. Overexpression of Oshox12 and Oshox14 in rice resulted in reduced panicle length and a dwarf phenotype. In addition, Oshox14 overexpression lines showed a deficiency in panicle exsertion. Our findings suggest that Oshox12 and Oshox14 may be involved in the regulation of panicle development. This study provides a significant advancement in understanding the functions of HD-Zip transcription factors in rice.
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Affiliation(s)
- Jingxia Shao
- College of Life Sciences, Northwest A&F University, Shaanxi, People’s Republic of China
- Institute of Biology (IBL), Leiden University, Leiden, The Netherlands
| | - Imran Haider
- Institute of Biology (IBL), Leiden University, Leiden, The Netherlands
- Laboratory of Plant Physiology, Wageningen University and Research Centre, Wageningen, The Netherlands
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Xiaoyi Zhu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops of Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, People’s Republic of China
| | | | - Elin Övernäs
- Department of Physiological Botany, EBC, Uppsala University, Uppsala, Sweden
| | | | - Gaisheng Zhang
- College of Agronomy, Northwest A&F University, Shaanxi, People’s Republic of China
| | - Mei Wang
- Institute of Biology (IBL), Leiden University, Leiden, The Netherlands
- Leiden University European Center for Chinese Medicine and Natural Compounds, Leiden, The Netherlands
| | - Harro J. Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research Centre, Wageningen, The Netherlands
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160
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Odonkor S, Choi S, Chakraborty D, Martinez-Bello L, Wang X, Bahri BA, Tenaillon MI, Panaud O, Devos KM. QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica. FRONTIERS IN PLANT SCIENCE 2018; 9:918. [PMID: 30073004 PMCID: PMC6060267 DOI: 10.3389/fpls.2018.00918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/11/2018] [Indexed: 05/13/2023]
Abstract
Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5'UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet.
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Affiliation(s)
- Sandra Odonkor
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Soyeon Choi
- Department of Genetics, University of Georgia, Athens, GA, United States
| | | | - Liliam Martinez-Bello
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Xuewen Wang
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Genetics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Bochra A. Bahri
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Laboratory of Bioagressors and Integrated Protection in Agriculture (LR14AGR02), The National Agronomic Institute of Tunisia, University of Carthage, Tunis, Tunisia
| | - Maud I. Tenaillon
- UMR8120 Génétique Quantitative et Evolution Le Moulon, Institut National de la Recherche Agronomique, Université Paris-Sud, Centre National de la Recherche Scientifique, AgroParisTech, Université Paris-Saclay, Paris, France
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR UPVD/CNRS, Université de Perpignan Via Domitia, Perpignan, France
| | - Katrien M. Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
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161
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Lister DL, Jones H, Oliveira HR, Petrie CA, Liu X, Cockram J, Kneale CJ, Kovaleva O, Jones MK. Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes. PLoS One 2018; 13:e0196652. [PMID: 30020920 PMCID: PMC6051582 DOI: 10.1371/journal.pone.0196652] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/17/2018] [Indexed: 11/19/2022] Open
Abstract
One of the world’s most important crops, barley, was domesticated in the Near East around 11,000 years ago. Barley is a highly resilient crop, able to grown in varied and marginal environments, such as in regions of high altitude and latitude. Archaeobotanical evidence shows that barley had spread throughout Eurasia by 2,000 BC. To further elucidate the routes by which barley cultivation was spread through Eurasia, simple sequence repeat (SSR) analysis was used to determine genetic diversity and population structure in three extant barley taxa: domesticated barley (Hordeum vulgare L. subsp. vulgare), wild barley (H. vulgare subsp. spontaneum) and a six-rowed brittle rachis form (H. vulgare subsp. vulgare f. agriocrithon (Åberg) Bowd.). Analysis of data using the Bayesian clustering algorithm InStruct suggests a model with three ancestral genepools, which captures a major split in the data, with substantial additional resolution provided under a model with eight genepools. Our results indicate that H. vulgare subsp. vulgare f. agriocrithon accessions and Tibetan Plateau H. vulgare subsp. spontaneum are closely related to the H. vulgare subsp. vulgare in their vicinity, and are therefore likely to be feral derivatives of H. vulgare subsp. vulgare. Under the eight genepool model, cultivated barley is split into six ancestral genepools, each of which has a distinct distribution through Eurasia, along with distinct morphological features and flowering time phenotypes. The distribution of these genepools and their phenotypic characteristics is discussed together with archaeological evidence for the spread of barley eastwards across Eurasia.
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Affiliation(s)
- Diane L. Lister
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | - Huw Jones
- The John Bingham Laboratory, NIAB, Cambridge, United Kingdom
| | - Hugo R. Oliveira
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Cameron A. Petrie
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
| | - Xinyi Liu
- Department of Anthropology, Washington University in St. Louis, St. Louis, MO, United States of America
| | - James Cockram
- The John Bingham Laboratory, NIAB, Cambridge, United Kingdom
| | - Catherine J. Kneale
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Olga Kovaleva
- N.I. Vavilov Research Institute of Plant Industry, St. Petersburg, Russia
| | - Martin K. Jones
- Department of Archaeology, University of Cambridge, Cambridge, United Kingdom
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162
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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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163
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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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164
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Pourkheirandish M, Kanamori H, Wu J, Sakuma S, Blattner FR, Komatsuda T. Elucidation of the origin of 'agriocrithon' based on domestication genes questions the hypothesis that Tibet is one of the centers of barley domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:525-534. [PMID: 29469199 DOI: 10.1111/tpj.13876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/12/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Wild barley forms a two-rowed spike with a brittle rachis whereas domesticated barley has two- or six-rowed spikes with a tough rachis. Like domesticated barley, 'agriocrithon' forms a six-rowed spike; however, the spike is brittle as in wild barley, which makes the origin of agriocrithon obscure. Haplotype analysis of the Six-rowed spike 1 (vrs1) and Non-brittle rachis 1 (btr1) and 2 (btr2) genes was conducted to infer the origin of agriocrithon barley. Some agriocrithon barley accessions (eu-agriocrithon) carried Btr1 and Btr2 haplotypes that are not found in any cultivars, implying that they are directly derived from wild barley through a mutation at the vrs1 locus. Other agriocrithon barley accessions (pseudo-agriocrithon) carried Btr1 or Btr2 from cultivated barley, thus implying that they originated from hybridization between six-rowed landraces carrying btr1Btr2 and Btr1btr2 genotypes followed by recombination to produce Btr1Btr2. All materials we collected from Tibet belong to pseudo-agriocrithon and thus do not support the Tibetan Plateau as being a center of barley domestication. Tracing the evolutionary history of these allelic variants revealed that eu-agriocrithon represents six-rowed barley lineages that were selected by early farmers, once in south-eastern Turkmenistan (vrs1.a1) and again in the eastern part of Uzbekistan (vrs1.a4).
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Affiliation(s)
- Mohammad Pourkheirandish
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Faculty of Science, Plant Breeding Institute, The University of Sydney, Cobbitty, NSW, 2570, Australia
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Jianzhong Wu
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Shun Sakuma
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
| | - Frank R Blattner
- Leibniz Institute of Plant Genetics and Crop Research (IPK), Gatersleben, D-06466, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, 305-8602, Japan
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, 305-8518, Japan
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165
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Henry IM, Akagi T, Tao R, Comai L. One Hundred Ways to Invent the Sexes: Theoretical and Observed Paths to Dioecy in Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:553-575. [PMID: 29719167 DOI: 10.1146/annurev-arplant-042817-040615] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Dioecy, the presence of male and female flowers on separate individuals, is both widespread and uncommon within flowering plants, with only a few percent of dioecious species spread across most major phylogenetic taxa. It is therefore safe to assume that dioecy evolved independently in these different groups, which allows us to ask questions regarding the molecular and developmental mechanisms underlying these independent transitions to dioecy. We start this review by examining the problem from the standpoint of a genetic engineer trying to develop dioecy, discuss various potential solutions, and compare them to models proposed in the past and based on genetic and evolutionary considerations. Next, we present recent information regarding candidate sex determinants in three species, acquired using newly established genomic approaches. Although such specific information is still scarce, it is slowly becoming apparent that various genes or pathways can be altered to evolve dioecy.
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Affiliation(s)
- Isabelle M Henry
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
| | - Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan; ,
| | - Luca Comai
- Department of Plant Biology, University of California, Davis, California 95616, USA; ,
- Genome Center, University of California, Davis, California 95616, USA
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166
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Xu X, Sharma R, Tondelli A, Russell J, Comadran J, Schnaithmann F, Pillen K, Kilian B, Cattivelli L, Thomas WTB, Flavell AJ. Genome-Wide Association Analysis of Grain Yield-Associated Traits in a Pan-European Barley Cultivar Collection. THE PLANT GENOME 2018; 11:170073. [PMID: 29505630 DOI: 10.3835/plantgenome2017.08.0073] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A collection of 379 Hordeum vulgare cultivars, comprising all combinations of spring and winter growth habits with two and six row ear type, was screened by genome wide association analysis to discover alleles controlling traits related to grain yield. Genotypes were obtained at 6,810 segregating gene-based single nucleotide polymorphism (SNP) loci and corresponding field trial data were obtained for eight traits related to grain yield at four European sites in three countries over two growth years. The combined data were analyzed and statistically significant associations between the traits and regions of the barley genomes were obtained. Combining this information with the high resolution gene map for barley allowed the identification of candidate genes underlying all scored traits and superposition of this information with the known genomics of grain trait genes in rice resulted in the assignation of 13 putative barley genes controlling grain traits in European cultivated barley. Several of these genes are associated with grain traits in both winter and spring barley.
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167
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MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway. Nat Commun 2018; 9:822. [PMID: 29483511 PMCID: PMC5826930 DOI: 10.1038/s41467-018-03238-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/26/2018] [Indexed: 01/08/2023] Open
Abstract
Grain number per panicle (GNP) is a major determinant of grain yield in cereals. However, the mechanisms that regulate GNP remain unclear. To address this issue, we isolate a series of sorghum [Sorghum bicolor (L.) Moench] multiseeded (msd) mutants that can double GNP by increasing panicle size and altering floral development so that all spikelets are fertile and set grain. Through bulk segregant analysis by next-generation sequencing, we identify MSD1 as a TCP (Teosinte branched/Cycloidea/PCF) transcription factor. Whole-genome expression profiling reveals that jasmonic acid (JA) biosynthetic enzymes are transiently activated in pedicellate spikelets. Young msd1 panicles have 50% less JA than wild-type (WT) panicles, and application of exogenous JA can rescue the msd1 phenotype. Our results reveal a new mechanism for increasing GNP, with the potential to boost grain yield, and provide insight into the regulation of plant inflorescence architecture and development. Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.
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168
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Giunta F, De Vita P, Mastrangelo AM, Sanna G, Motzo R. Environmental and Genetic Variation for Yield-Related Traits of Durum Wheat as Affected by Development. FRONTIERS IN PLANT SCIENCE 2018; 9:8. [PMID: 29403518 PMCID: PMC5778143 DOI: 10.3389/fpls.2018.00008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/03/2018] [Indexed: 05/27/2023]
Abstract
Phenology has a profound effect on adaptation and productivity of crops. The impact of phenology on tillering and fertility traits of durum wheat (Triticum turgidum L. subsp. durum Desf.) was evaluated with the aim of specifying which group of flowering genes (Vrn, Ppd, or eps) was involved in their control. A recombinant inbred line population was grown under four contrasting conditions of vernalization and daylength. Phenotyping was carried out according to robust phenological models dissecting both phenological and yield related traits. Whole-genome profiling was performed using the DArT-Seq technology. The genetic variability for tillering was mainly related to the genetic variability for vernalization sensitivity, as shown by the many quantitative trait loci (QTLs) identified in non-vernalized plants associated to both tillering and phenological traits. No effects of photoperiod sensitivity on spikelet number were detected in short-day-grown plants, apparently because of limited genetic variability in photoperiod sensitivity of the population. Earliness per se was involved in control of spikelet number via final leaf number, with these traits genetically correlated and sharing some QTLs. Chaff weight and number of kernels per g chaff were negatively associated and related to anthesis date under most conditions. QTL mapping uncovered novel loci involved in phenological control of tillering and fertility traits, and confirmed the presence of several well-established loci. Phenotyping of both phenology and kernel number according to a robust physiological model amplified the possibility of identifying genetic factors underlying their variations. Also, isolating known flowering gene cues by manipulation of environmental conditions provided the opportunity for each group of genes to be expressed without confounding effects of the others. This information helps to predict the consequences of either genetic manipulation of flowering genes and changes in environmental conditions on the potential yield of durum wheat.
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Affiliation(s)
- Francesco Giunta
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Pasquale De Vita
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Foggia, Italy
| | - Anna M. Mastrangelo
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Foggia, Italy
- Consiglio per la Ricerca in Agricoltura e L'analisi Dell'economia Agraria-Centro Cerealicoltura e Colture Industriali (CREA-CI), Bergamo, Italy
| | - Gavino Sanna
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - Rosella Motzo
- Sez. Agronomia, Coltivazioni erbacee e Genetica, Dipartimento di Agraria, University of Sassari, Sassari, Italy
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Hu X, Zuo J, Wang J, Liu L, Sun G, Li C, Ren X, Sun D. Multi-Locus Genome-Wide Association Studies for 14 Main Agronomic Traits in Barley. FRONTIERS IN PLANT SCIENCE 2018; 9:1683. [PMID: 30524459 PMCID: PMC6257129 DOI: 10.3389/fpls.2018.01683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/29/2018] [Indexed: 05/02/2023]
Abstract
The agronomic traits, including morphological and yield component traits, are important in barley breeding programs. In order to reveal the genetic foundation of agronomic traits of interest, in this study 122 doubled haploid lines from a cross between cultivars "Huaai 11" (six-rowed and dwarf) and "Huadamai 6" (two-rowed) were genotyped by 9680 SNPs and phenotyped 14 agronomic traits in 3 years, and the two datasets were used to conduct multi-locus genome-wide association studies. As a result, 913 quantitative trait nucleotides (QTNs) were identified by five multi-locus GWAS methods to be associated with the above 14 traits and their best linear unbiased predictions. Among these QTNs and their adjacent genes, 39 QTNs (or QTN clusters) were repeatedly detected in various environments and methods, and 10 candidate genes were identified from gene annotation. Nineteen QTNs and two genes (sdw1/denso and Vrs1) were previously reported, and eight candidate genes need to be further validated. The Vrs1 gene, controlling the number of rows in the spike, was found to be associated with spikelet number of main spike, spikelet number per plant, grain number per plant, grain number per spike, and 1,000 grain weight in multiple environments and by multi-locus GWAS methods. Therefore, the above results evidenced the feasibility and reliability of genome-wide association studies in doubled haploid population, and the QTNs and their candidate genes detected in this study are useful for marker-assisted selection breeding, gene cloning, and functional identification in barley.
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Affiliation(s)
- Xin Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guiyang College of Traditional Chinese Medicine, Guiyang, China
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jibin Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lipan Liu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, NS, Canada
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Xifeng Ren
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Center for Grain Industry, Jingzhou, China
- *Correspondence: Dongfa Sun
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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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173
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Teplyakova S, Lebedeva M, Ivanova N, Horeva V, Voytsutskaya N, Kovaleva O, Potokina E. Impact of the 7-bp deletion in HvGA20ox2 gene on agronomic important traits in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2017; 17:181. [PMID: 29143605 PMCID: PMC5688404 DOI: 10.1186/s12870-017-1121-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alike to Reduced height-1 (Rht-1) genes in wheat and the semi dwarfing (sd-1) gene in rice, the sdw1/denso locus involved in the metabolism of the GA, was designated as the 'Green Revolution' gene in barley. The recent molecular characterization of the candidate gene HvGA20ox2 for sdw1/denso locus allows to estimate the impact of the functional polymorphism of this gene on the variation of agronomically important traits in barley. RESULTS We investigated the effect of the 7-bp deletion in exon 1 of HvGA20ox2 gene (sdw1.d mutation) on the variation of yield-related and malting quality traits in the population of DHLs derived from cross of medium tall barley Morex and semi-dwarf barley Barke. Segregation of plant height, flowering time, thousand grain weight, grain protein content and grain starch was evaluated in two diverse environments separated from one another by 15° of latitude. The 7-bp deletion in HvGA20ox2 gene reduced plant height by approximately 13 cm and delayed flowering time by 3-5 days in the barley segregating DHLs population independently on environmental cue. On other hand, the sdw1.d mutation did not affect significantly either grain quality traits (protein and starch content) or thousand grain weight. CONCLUSIONS The beneficial effect of the sdw1.d allele could be associated in barley with lodging resistance and extended period of vegetative growth allowing to accumulate additional biomass that supports higher yield in certain environments. However, no direct effect of the sdw1.d mutation on thousand grain weight or grain quality traits in barley was detected.
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Affiliation(s)
- Serafima Teplyakova
- Saint Petersburg State University, Universitetskaya emb.7/9, St. Petersburg, 199034, Russia
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Marina Lebedeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia
| | - Nadezhda Ivanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Valentina Horeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Nina Voytsutskaya
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Olga Kovaleva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Elena Potokina
- Saint Petersburg State University, Universitetskaya emb.7/9, St. Petersburg, 199034, Russia.
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.
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174
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Bengtsson T, Åhman I, Manninen O, Reitan L, Christerson T, Due Jensen J, Krusell L, Jahoor A, Orabi J. A Novel QTL for Powdery Mildew Resistance in Nordic Spring Barley ( Hordeum vulgare L. ssp. vulgare) Revealed by Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2017; 8:1954. [PMID: 29184565 PMCID: PMC5694554 DOI: 10.3389/fpls.2017.01954] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/30/2017] [Indexed: 05/26/2023]
Abstract
The powdery mildew fungus, Blumeria graminis f. sp. hordei is a worldwide threat to barley (Hordeum vulgare L. ssp. vulgare) production. One way to control the disease is by the development and deployment of resistant cultivars. A genome-wide association study was performed in a Nordic spring barley panel consisting of 169 genotypes, to identify marker-trait associations significant for powdery mildew. Powdery mildew was scored during three years (2012-2014) in four different locations within the Nordic region. There were strong correlations between data from all locations and years. In total four QTLs were identified, one located on chromosome 4H in the same region as the previously identified mlo locus and three on chromosome 6H. Out of these three QTLs identified on chromosome 6H, two are in the same region as previously reported QTLs for powdery mildew resistance, whereas one QTL appears to be novel. The top NCBI BLASTn hit of the SNP markers within the novel QTL predicted the responsible gene to be the 26S proteasome regulatory subunit, RPN1, which is required for innate immunity and powdery mildew-induced cell death in Arabidopsis. The results from this study have revealed SNP marker candidates that can be exploited for use in marker-assisted selection and stacking of genes for powdery mildew resistance in barley.
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Affiliation(s)
- Therése Bengtsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Inger Åhman
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | | | | | | | | | - Ahmed Jahoor
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Nordic Seed A/S, Galten, Denmark
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175
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Li C, Chen G, Mishina K, Yamaji N, Ma JF, Yukuhiro F, Tagiri A, Liu C, Pourkheirandish M, Anwar N, Ohta M, Zhao P, Lundqvist U, Li X, Komatsuda T. A GDSL-motif esterase/acyltransferase/lipase is responsible for leaf water retention in barley. PLANT DIRECT 2017; 1:e00025. [PMID: 31245672 PMCID: PMC6508521 DOI: 10.1002/pld3.25] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 09/21/2017] [Accepted: 10/06/2017] [Indexed: 05/19/2023]
Abstract
The hydrophobic cuticle covers the surface of the most aerial organs of land plants. The barley mutant eceriferum-zv (cer-zv), which is hypersensitive to drought, is unable to accumulate a sufficient quantity of cutin in its leaf cuticle. The mutated locus has been mapped to a 0.02 cM segment in the pericentromeric region of chromosome 4H. As a map-based cloning approach to isolate the gene was therefore considered unlikely to be feasible, a comparison was instead made between the transcriptomes of the mutant and the wild type. In conjunction with extant genomic information, on the basis of predicted functionality, only two genes were considered likely to encode a product associated with cutin formation. When eight independent cer-zv mutant alleles were resequenced with respect to the two candidate genes, it was confirmed that the gene underlying the mutation in each allele encodes a Gly-Asp-Ser-Leu (GDSL)-motif esterase/acyltransferase/lipase. The gene was transcribed in the epidermis, and its product was exclusively deposited in cell wall at the boundary of the cuticle in the leaf elongation zone, coinciding with the major site of cutin deposition. CER-ZV is speculated to function in the deposition of cutin polymer. Its homologs were found in green algae, moss, and euphyllophytes, indicating that it is highly conserved in plant kingdom.
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Affiliation(s)
- Chao Li
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Shanghai Key Laboratory of Plant Functional Genomics and ResourcesShanghai Chenshan Botanical GardenShanghaiChina
- Shanghai Chenshan Plant Science Research CenterChinese Academy of SciencesShanghaiChina
| | - Guoxiong Chen
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Kohei Mishina
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
| | - Naoki Yamaji
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan
| | - Jian Feng Ma
- Institute of Plant Science and ResourcesOkayama UniversityKurashikiJapan
| | - Fumiko Yukuhiro
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Akemi Tagiri
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Cheng Liu
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Crop Research InstituteShandong Academy of Agricultural SciencesJi'nanChina
| | - Mohammad Pourkheirandish
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Faculty of Agriculture and EnvironmentPlant Breeding InstituteThe University of SydneyCobbittyNSWAustralia
| | - Nadia Anwar
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
| | - Masaru Ohta
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
| | - Pengshan Zhao
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | | | - Xinrong Li
- Key Laboratory of Stress Physiology and Ecology in Cold and Arid RegionsGansu ProvinceChina
- Northwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
- Shapotou Desert Research and Experimental StationNorthwest Institute of Eco‐Environment and ResourcesChinese Academy of SciencesLanzhouChina
| | - Takao Komatsuda
- National Institute of Agrobiological SciencesTsukubaIbarakiJapan
- Institute of Crop ScienceNAROKannondaiTsukubaIbarakiJapan
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176
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Bull H, Casao MC, Zwirek M, Flavell AJ, Thomas WTB, Guo W, Zhang R, Rapazote-Flores P, Kyriakidis S, Russell J, Druka A, McKim SM, Waugh R. Barley SIX-ROWED SPIKE3 encodes a putative Jumonji C-type H3K9me2/me3 demethylase that represses lateral spikelet fertility. Nat Commun 2017; 8:936. [PMID: 29038434 PMCID: PMC5643332 DOI: 10.1038/s41467-017-00940-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 07/29/2017] [Indexed: 11/30/2022] Open
Abstract
The barley inflorescence (spike) comprises a multi-noded central stalk (rachis) with tri-partite clusters of uni-floretted spikelets attached alternately along its length. Relative fertility of lateral spikelets within each cluster leads to spikes with two or six rows of grain, or an intermediate morphology. Understanding the mechanisms controlling this key developmental step could provide novel solutions to enhanced grain yield. Classical genetic studies identified five major SIX-ROWED SPIKE (VRS) genes, with four now known to encode transcription factors. Here we identify and characterise the remaining major VRS gene, VRS3, as encoding a putative Jumonji C-type H3K9me2/me3 demethylase, a regulator of chromatin state. Exploring the expression network modulated by VRS3 reveals specific interactions, both with other VRS genes and genes involved in stress, hormone and sugar metabolism. We show that combining a vrs3 mutant allele with natural six-rowed alleles of VRS1 and VRS5 leads to increased lateral grain size and greater grain uniformity. The VRS genes of barley control the fertility of the lateral spikelets on the barley inflorescence. Here, Bull et al. show that VRS3 encodes a putative Jumonji C-type histone demethylase that regulates expression of other VRS genes, and genes involved in stress, hormone and sugar metabolism.
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Affiliation(s)
- Hazel Bull
- James Hutton Limited, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.,Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - M Cristina Casao
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Monika Zwirek
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Andrew J Flavell
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - William T B Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Wenbin Guo
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.,Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Runxuan Zhang
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Paulo Rapazote-Flores
- Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Stylianos Kyriakidis
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Arnis Druka
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland
| | - Sarah M McKim
- Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland. .,Division of Plant Sciences, School of Life Sciences, The University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, Scotland.
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177
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Smith O, Palmer SA, Clapham AJ, Rose P, Liu Y, Wang J, Allaby RG. Small RNA Activity in Archeological Barley Shows Novel Germination Inhibition in Response to Environment. Mol Biol Evol 2017; 34:2555-2562. [PMID: 28655202 PMCID: PMC5850308 DOI: 10.1093/molbev/msx175] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The recovery of ancient RNA from archeological material could enable the direct study of microevolutionary processes. Small RNAs are a rich source of information because their small size is compatible with biomolecular preservation, and their roles in gene regulation make them likely foci of evolutionary change. We present here the small RNA fraction from a sample of archeological barley generated using high-throughput sequencing that has previously been associated with localized adaptation to drought. Its microRNA profile is broadly similar to 19 globally distributed modern barley samples with the exception of three microRNAs (miRNA159, miRNA319, and miR396), all of which are known to have variable expression under stress conditions. We also found retrotransposon activity to be significantly reduced in the archeological barley compared with the controls, where one would expect the opposite under stress conditions. We suggest that the archeological barley's conflicting stress signals could be the result of long-term adaptation to its local environment.
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Affiliation(s)
- Oliver Smith
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Sarah A. Palmer
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Alan J. Clapham
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
| | - Pamela Rose
- The Austrian Archaeological Institute, Cairo Branch, Zamalek, Cairo, Egypt
| | - Yuan Liu
- BGI-Europe-UK, London, United Kingdom
| | | | - Robin G. Allaby
- School of Life Sciences, The University of Warwick, Coventry, United Kingdom
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178
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Wang Y, Yu H, Tian C, Sajjad M, Gao C, Tong Y, Wang X, Jiao Y. Transcriptome Association Identifies Regulators of Wheat Spike Architecture. PLANT PHYSIOLOGY 2017; 175:746-757. [PMID: 28807930 PMCID: PMC5619896 DOI: 10.1104/pp.17.00694] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/11/2017] [Indexed: 05/20/2023]
Abstract
The architecture of wheat (Triticum aestivum) inflorescence and its complexity is among the most important agronomic traits that influence yield. For example, wheat spikes vary considerably in the number of spikelets, which are specialized reproductive branches, and the number of florets, which are spikelet branches that produce seeds. The large and repetitive nature of the three homologous and highly similar subgenomes of wheat has impeded attempts at using genetic approaches to uncover beneficial alleles that can be utilized for yield improvement. Using a population-associative transcriptomic approach, we analyzed the transcriptomes of developing spikes in 90 wheat lines comprising 74 landrace and 16 elite varieties and correlated expression with variations in spike complexity traits. In combination with coexpression network analysis, we inferred the identities of genes related to spike complexity. Importantly, further experimental studies identified regulatory genes whose expression is associated with and influences spike complexity. The associative transcriptomic approach utilized in this study allows rapid identification of the genetic basis of important agronomic traits in crops with complex genomes.
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Affiliation(s)
- Yuange Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haopeng Yu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caihuan Tian
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Muhammad Sajjad
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yiping Tong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangfeng Wang
- Department of Crop Genomics and Bioinformatics, College of Agronomy and Biotechnology, National Maize Improvement Center of China, China Agricultural University, Beijing 100193, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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179
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Mathan J, Bhattacharya J, Ranjan A. Enhancing crop yield by optimizing plant developmental features. Development 2017; 143:3283-94. [PMID: 27624833 DOI: 10.1242/dev.134072] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.
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Affiliation(s)
- Jyotirmaya Mathan
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Juhi Bhattacharya
- National Institute of Plant Genome Research, New Delhi 110067, India
| | - Aashish Ranjan
- National Institute of Plant Genome Research, New Delhi 110067, India
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180
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van Esse GW, Walla A, Finke A, Koornneef M, Pecinka A, von Korff M. Six-Rowed Spike3 (VRS3) Is a Histone Demethylase That Controls Lateral Spikelet Development in Barley. PLANT PHYSIOLOGY 2017; 174:2397-2408. [PMID: 28655778 PMCID: PMC5543938 DOI: 10.1104/pp.17.00108] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/25/2017] [Indexed: 05/17/2023]
Abstract
The complex nature of crop genomes has long prohibited the efficient isolation of agronomically relevant genes. However, recent advances in next-generation sequencing technologies provide new ways to accelerate fine-mapping and gene isolation in crops. We used RNA sequencing of allelic six-rowed spike3 (vrs3) mutants with altered spikelet development for gene identification and functional analysis in barley (Hordeum vulgare). Variant calling in two allelic vrs3 mutants revealed that VRS3 encodes a putative histone Lys demethylase with a conserved zinc finger and Jumonji C and N domain. Sanger sequencing of this candidate gene in independent allelic vrs3 mutants revealed a series of mutations in conserved domains, thus confirming our candidate as the VRS3 gene and suggesting that the row type in barley is determined epigenetically. Global transcriptional profiling in developing shoot apical meristems of vrs3 suggested that VRS3 acts as a transcriptional activator of the row-type genes VRS1 (Hv.HOMEOBOX1) and INTERMEDIUM-C (INT-C; Hv.TEOSINTE BRANCHED1). Comparative transcriptome analysis of the row-type mutants vrs3, vrs4 (Hv.RAMOSA2), and int-c confirmed that all three genes act as transcriptional activators of VRS1 and quantitative variation in the expression levels of VRS1 in these mutants correlated with differences in the number of developed lateral spikelets. The identification of genes and pathways affecting seed number in small grain cereals will enable to further unravel the transcriptional networks controlling this important yield component.
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Affiliation(s)
- G Wilma van Esse
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Agatha Walla
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
| | - Andreas Finke
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maarten Koornneef
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Ales Pecinka
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Maria von Korff
- Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Institute for Plant Genetics, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany
- Cluster of Excellence in Plant Sciences, Heinrich-Heine-Universität Düsseldorf, 40255 Düsseldorf, Germany
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181
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Thirulogachandar V, Alqudah AM, Koppolu R, Rutten T, Graner A, Hensel G, Kumlehn J, Bräutigam A, Sreenivasulu N, Schnurbusch T, Kuhlmann M. Leaf primordium size specifies leaf width and vein number among row-type classes in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 91:601-612. [PMID: 28482117 DOI: 10.1111/tpj.13590] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 04/20/2017] [Accepted: 04/27/2017] [Indexed: 05/18/2023]
Abstract
Exploring genes with impact on yield-related phenotypes is the preceding step to accomplishing crop improvements while facing a growing world population. A genome-wide association scan on leaf blade area (LA) in a worldwide spring barley collection (Hordeum vulgare L.), including 125 two- and 93 six-rowed accessions, identified a gene encoding the homeobox transcription factor, Six-rowed spike 1 (VRS1). VRS1 was previously described as a key domestication gene affecting spike development. Its mutation converts two-rowed (wild-type VRS1, only central fertile spikelets) into six-rowed spikes (mutant vrs1, fully developed fertile central and lateral spikelets). Phenotypic analyses of mutant and wild-type leaves revealed that mutants had an increased leaf width with more longitudinal veins. The observed significant increase of LA and leaf nitrogen (%) during pre-anthesis development in vrs1 mutants also implies a link between wider leaf and grain number, which was validated from the association of vrs1 locus with wider leaf and grain number. Histological and gene expression analyses indicated that VRS1 might influence the size of leaf primordia by affecting cell proliferation of leaf primordial cells. This finding was supported by the transcriptome analysis of mutant and wild-type leaf primordia where in the mutant transcriptional activation of genes related to cell proliferation was detectable. Here we show that VRS1 has an independent role on barley leaf development which might influence the grain number.
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Affiliation(s)
- Venkatasubbu Thirulogachandar
- Independent Junior Research Group Abiotic Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
- Interdisciplinary Centre for Crop Plant Research (IZN), Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Ahmad M Alqudah
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Ravi Koppolu
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Twan Rutten
- Research Group Structural Cell Biology, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Andreas Graner
- Research Group Genome Diversity, Department Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Goetz Hensel
- Research Group Plant Reproductive Biology, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Jochen Kumlehn
- Research Group Plant Reproductive Biology, Department Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Andrea Bräutigam
- Research Group Network Analysis and Modeling, Department Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Nese Sreenivasulu
- Independent Junior Research Group Abiotic Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
- Interdisciplinary Centre for Crop Plant Research (IZN), Hoher Weg 8, 06120, Halle (Saale), Germany
| | - Thorsten Schnurbusch
- HEISENBERG-Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Markus Kuhlmann
- Independent Junior Research Group Abiotic Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), Corrensstr. 3 06466 Stadt Seeland, OT Gatersleben, Germany
- Interdisciplinary Centre for Crop Plant Research (IZN), Hoher Weg 8, 06120, Halle (Saale), Germany
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182
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Selection During Maize Domestication Targeted a Gene Network Controlling Plant and Inflorescence Architecture. Genetics 2017; 207:755-765. [PMID: 28754660 DOI: 10.1534/genetics.117.300071] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 01/11/2023] Open
Abstract
Selection during evolution, whether natural or artificial, acts through the phenotype. For multifaceted phenotypes such as plant and inflorescence architecture, the underlying genetic architecture is comprised of a complex network of interacting genes rather than single genes that act independently to determine the trait. As such, selection acts on entire gene networks. Here, we begin to define the genetic regulatory network to which the maize domestication gene, teosinte branched1 (tb1), belongs. Using a combination of molecular methods to uncover either direct or indirect regulatory interactions, we identified a set of genes that lie downstream of tb1 in a gene network regulating both plant and inflorescence architecture. Additional genes, known from the literature, also act in this network. We observed that tb1 regulates both core cell cycle genes and another maize domestication gene, teosinte glume architecture1 (tga1). We show that several members of the MADS-box gene family are either directly or indirectly regulated by tb1 and/or tga1, and that tb1 sits atop a cascade of transcriptional regulators controlling both plant and inflorescence architecture. Multiple members of the tb1 network appear to have been the targets of selection during maize domestication. Knowledge of the regulatory hierarchies controlling traits is central to understanding how new morphologies evolve.
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183
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Abstract
A defining characteristic of grasses, including major cereal crops, is the way in which flowers are arranged on an inflorescence. A new study finds that regulation of hormone levels during development is crucial for determining the arrangement of flowers on a barley inflorescence, opening new doors for increasing grain yield.
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Affiliation(s)
- Scott A Boden
- John Innes Centre, Norwich Research Park, Norwich, UK
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184
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Nadolska-Orczyk A, Rajchel IK, Orczyk W, Gasparis S. Major genes determining yield-related traits in wheat and barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1081-1098. [PMID: 28314933 PMCID: PMC5440550 DOI: 10.1007/s00122-017-2880-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 02/17/2017] [Indexed: 05/20/2023]
Abstract
Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.
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Affiliation(s)
- Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Izabela K Rajchel
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Sebastian Gasparis
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
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185
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Barley Developmental Mutants: The High Road to Understand the Cereal Spike Morphology. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9020021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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186
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Østerberg JT, Xiang W, Olsen LI, Edenbrandt AK, Vedel SE, Christiansen A, Landes X, Andersen MM, Pagh P, Sandøe P, Nielsen J, Christensen SB, Thorsen BJ, Kappel K, Gamborg C, Palmgren M. Accelerating the Domestication of New Crops: Feasibility and Approaches. TRENDS IN PLANT SCIENCE 2017; 22:373-384. [PMID: 28262427 DOI: 10.1016/j.tplants.2017.01.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 12/09/2016] [Accepted: 01/16/2017] [Indexed: 05/19/2023]
Abstract
The domestication of new crops would promote agricultural diversity and could provide a solution to many of the problems associated with intensive agriculture. We suggest here that genome editing can be used as a new tool by breeders to accelerate the domestication of semi-domesticated or even wild plants, building a more varied foundation for the sustainable provision of food and fodder in the future. We examine the feasibility of such plants from biological, social, ethical, economic, and legal perspectives.
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Affiliation(s)
- Jeppe Thulin Østerberg
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Wen Xiang
- Center for Public Regulation and Administration, Faculty of Law, University of Copenhagen, Studiestræde 6, 1455 Copenhagen K, Denmark
| | - Lene Irene Olsen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Anna Kristina Edenbrandt
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Suzanne Elizabeth Vedel
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Andreas Christiansen
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, 2300 Copenhagen S, Denmark
| | - Xavier Landes
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, 2300 Copenhagen S, Denmark
| | - Martin Marchman Andersen
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, 2300 Copenhagen S, Denmark
| | - Peter Pagh
- Center for Public Regulation and Administration, Faculty of Law, University of Copenhagen, Studiestræde 6, 1455 Copenhagen K, Denmark
| | - Peter Sandøe
- Department of Large Animal Sciences, University of Copenhagen, 1870 Frederiksberg C, Denmark
| | - John Nielsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Østerbro, Denmark
| | - Søren Brøgger Christensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Østerbro, Denmark
| | - Bo Jellesmark Thorsen
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Klemens Kappel
- Department of Media, Cognition, and Communication, University of Copenhagen, Karen Blixens Vej 4, 2300 Copenhagen S, Denmark
| | - Christian Gamborg
- Department of Food and Resource Economics, University of Copenhagen, Rolighedsvej 23, 1958 Frederiksberg C, Denmark
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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187
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Guo Z, Chen D, Alqudah AM, Röder MS, Ganal MW, Schnurbusch T. Genome-wide association analyses of 54 traits identified multiple loci for the determination of floret fertility in wheat. THE NEW PHYTOLOGIST 2017; 214:257-270. [PMID: 27918076 DOI: 10.1111/nph.14342] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/17/2016] [Indexed: 05/18/2023]
Abstract
Increasing grain yield is still the main target of wheat breeding; yet today's wheat plants utilize less than half of their yield potential. Owing to the difficulty of determining grain yield potential in a large population, few genetic factors regulating floret fertility (i.e. the difference between grain yield potential and grain number) have been reported to date. In this study, we conducted a genome-wide association study (GWAS) by quantifying 54 traits (16 floret fertility traits and 38 traits for assimilate partitioning and spike morphology) in 210 European winter wheat accessions. The results of this GWAS experiment suggested potential associations between floret fertility, assimilate partitioning and spike morphology revealed by shared quantitative trait loci (QTLs). Several candidate genes involved in carbohydrate metabolism, phytohormones or floral development colocalized with such QTLs, thereby providing potential targets for selection. Based on our GWAS results we propose a genetic network underlying floret fertility and related traits, nominating determinants for improved yield performance.
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Affiliation(s)
- Zifeng Guo
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Dijun Chen
- Research Group Image Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Ahmad M Alqudah
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Marion S Röder
- Research Group Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
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188
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Shang Y, Yang F, Schulman AH, Zhu J, Jia Y, Wang J, Zhang XQ, Jia Q, Hua W, Yang J, Li C. Gene Deletion in Barley Mediated by LTR-retrotransposon BARE. Sci Rep 2017; 7:43766. [PMID: 28252053 PMCID: PMC5333098 DOI: 10.1038/srep43766] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/27/2017] [Indexed: 11/13/2022] Open
Abstract
A poly-row branched spike (prbs) barley mutant was obtained from soaking a two-rowed barley inflorescence in a solution of maize genomic DNA. Positional cloning and sequencing demonstrated that the prbs mutant resulted from a 28 kb deletion including the inflorescence architecture gene HvRA2. Sequence annotation revealed that the HvRA2 gene is flanked by two LTR (long terminal repeat) retrotransposons (BARE) sharing 89% sequence identity. A recombination between the integrase (IN) gene regions of the two BARE copies resulted in the formation of an intact BARE and loss of HvRA2. No maize DNA was detected in the recombination region although the flanking sequences of HvRA2 gene showed over 73% of sequence identity with repetitive sequences on 10 maize chromosomes. It is still unknown whether the interaction of retrotransposons between barley and maize has resulted in the recombination observed in the present study.
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Affiliation(s)
- Yi Shang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Fei Yang
- Department of Genetics and Cell Biology, Yangtze University, Jingzhou, Hubei 434023, China
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Alan H. Schulman
- Luke/BI Plant Genomics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, FIN-00014 Helsinki, Finland
- Green Technology, Natural Resources Institute Finland (Luke), Viikinkaari 1, FIN-00790 Helsinki, Finland
| | - Jinghuan Zhu
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Yong Jia
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Junmei Wang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
| | - Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wei Hua
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Jianming Yang
- National Barley Improvement Centre, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou 310021, China
| | - Chengdao Li
- Department of Genetics and Cell Biology, Yangtze University, Jingzhou, Hubei 434023, China
- Western Barley Genetics Alliance, Murdoch University, 90 South Street, Murdoch WA 6150, Australia
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189
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Patterns of Evolutionary Trajectories and Domestication History within the Genus Hordeum Assessed by REMAP Markers. J Mol Evol 2017; 84:116-128. [PMID: 28168328 DOI: 10.1007/s00239-016-9779-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 12/29/2016] [Indexed: 10/20/2022]
Abstract
The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley. The obtained data are consistent with the current taxonomic status within the genus Hordeum. Similar level of genetic diversity was observed between the wild and the domesticated barley accessions suggesting that transposable elements` activity and accumulation may counteract the decrease of genome-wide diversity following domestication. In addition, eco-geographical sub-genome pools of the cultivated barley were identified in support to the theory of multiple origins of domestication within the genus Hordeum. We also provide conclusions about the relationship between accessions of different species and the putative routes of barley domestication. In conclusion, the retrotransposon BARE-1 stands as a reliable and perspective DNA marker for the assessment of the phylogenetic and domestication history in the genus Hordeum and other crop species.
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190
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Abstract
Background Barley seed proteins are of prime importance to the brewing industry, human and animal nutrition and in plant breeding for cultivar identification. To obtain comprehensive proteomic data from seeds, total protein from a two-rowed (Conrad) and a six-rowed (Lacey) barley cultivar were precipitated in acetone, digested in-solution, and the resulting peptides were analyzed by nano-liquid chromatography coupled with tandem mass spectrometry. Results The raw mass spectra data searched against Uniprot’s Barley database using in-house Mascot search engine identified 1168 unique proteins. Gene Ontology (GO) analysis indicated that the majority of the seed proteins were cytosolic, with catalytic activity and associated with carbohydrate metabolism. Spectral counting analysis showed that there are 20 differentially abundant seed proteins between the two-rowed Conrad and six-rowed Lacey cultivars. Conclusion This study paves the way for the use of a top-down gel-free proteomics strategy in barley for investigating more complex traits such as malting quality. Differential abundance of hordoindoline proteins impact the seed hardness trait of barley cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3408-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ramamurthy Mahalingam
- USDA, Agricultural Research Service, Cereal Crops Research Unit, 502 Walnut Street, Madison, WI, 53726, USA.
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191
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Yang CJ, Kursel LE, Studer AJ, Bartlett ME, Whipple CJ, Doebley JF. A Gene for Genetic Background in Zea mays: Fine-Mapping enhancer of teosinte branched1.2 to a YABBY Class Transcription Factor. Genetics 2016; 204:1573-1585. [PMID: 27729422 PMCID: PMC5161286 DOI: 10.1534/genetics.116.194928] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 09/28/2016] [Indexed: 01/08/2023] Open
Abstract
The effects of an allelic substitution at a gene often depend critically on genetic background, i.e., the genotypes at other genes in the genome. During the domestication of maize from its wild ancestor (teosinte), an allelic substitution at teosinte branched (tb1) caused changes in both plant and ear architecture. The effects of tb1 on phenotype were shown to depend on multiple background loci, including one called enhancer of tb1.2 (etb1.2). We mapped etb1.2 to a YABBY class transcription factor (ZmYAB2.1) and showed that the maize alleles of ZmYAB2.1 are either expressed at a lower level than teosinte alleles or disrupted by insertions in the sequences. tb1 and etb1.2 interact epistatically to control the length of internodes within the maize ear, which affects how densely the kernels are packed on the ear. The interaction effect is also observed at the level of gene expression, with tb1 acting as a repressor of ZmYAB2.1 expression. Curiously, ZmYAB2.1 was previously identified as a candidate gene for another domestication trait in maize, nonshattering ears. Consistent with this proposed role, ZmYAB2.1 is expressed in a narrow band of cells in immature ears that appears to represent a vestigial abscission (shattering) zone. Expression in this band of cells may also underlie the effect on internode elongation. The identification of ZmYAB2.1 as a background factor interacting with tb1 is a first step toward a gene-level understanding of how tb1 and the background within which it works evolved in concert during maize domestication.
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Affiliation(s)
- Chin Jian Yang
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Lisa E Kursel
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Anthony J Studer
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | | | | | - John F Doebley
- Laboratory of Genetics, University of Wisconsin-Madison, Wisconsin 53706
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192
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Akagi T, Henry IM, Kawai T, Comai L, Tao R. Epigenetic Regulation of the Sex Determination Gene MeGI in Polyploid Persimmon. THE PLANT CELL 2016; 28:2905-2915. [PMID: 27956470 PMCID: PMC5240738 DOI: 10.1105/tpc.16.00532] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/28/2016] [Accepted: 12/10/2016] [Indexed: 05/20/2023]
Abstract
Epigenetic regulation can add a flexible layer to genetic variation, potentially enabling long-term but reversible cis-regulatory changes to an allele while maintaining its DNA sequence. Here, we present a case in which alternative epigenetic states lead to reversible sex determination in the hexaploid persimmon Diospyros kaki Previously, we elucidated the molecular mechanism of sex determination in diploid persimmon and demonstrated the action of a Y-encoded sex determinant pseudogene called OGI, which produces small RNAs targeting the autosomal gene MeGI, resulting in separate male and female individuals (dioecy). We contrast these findings with the discovery, in hexaploid persimmon, of an additional layer of regulation in the form of DNA methylation of the MeGI promoter associated with the production of both male and female flowers in genetically male trees. Consistent with this model, developing male buds exhibited higher methylation levels across the MeGI promoter than developing female flowers from either monoecious or female trees. Additionally, a DNA methylation inhibitor induced developing male buds to form feminized flowers. Concurrently, in Y-chromosome-carrying trees, the expression of OGI is silenced by the presence of a SINE (short interspersed nuclear element)-like insertion in the OGI promoter. Our findings provide an example of an adaptive scenario involving epigenetic plasticity.
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Affiliation(s)
- Takashi Akagi
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
- JST, PRESTO, Kawaguchi-shi, Saitama 332-0012, Japan
| | - Isabelle M Henry
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Takashi Kawai
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Luca Comai
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Ryutaro Tao
- Laboratory of Pomology, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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193
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Youssef HM, Eggert K, Koppolu R, Alqudah AM, Poursarebani N, Fazeli A, Sakuma S, Tagiri A, Rutten T, Govind G, Lundqvist U, Graner A, Komatsuda T, Sreenivasulu N, Schnurbusch T. VRS2 regulates hormone-mediated inflorescence patterning in barley. Nat Genet 2016; 49:157-161. [PMID: 27841879 DOI: 10.1038/ng.3717] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 10/17/2016] [Indexed: 12/20/2022]
Abstract
Plant architecture has clear agronomic and economic implications for crops such as wheat and barley, as it is a critical factor for determining grain yield. Despite this, only limited molecular information is available about how grain-bearing inflorescences, called spikes, are formed and maintain their regular, distichous pattern. Here we elucidate the molecular and hormonal role of Six-rowed spike 2 (Vrs2), which encodes a SHORT INTERNODES (SHI) transcriptional regulator during barley inflorescence and shoot development. We show that Vrs2 is specifically involved in floral organ patterning and phase duration by maintaining hormonal homeostasis and gradients during normal spike development and similarly influences plant stature traits. Furthermore, we establish a link between the SHI protein family and sucrose metabolism during organ growth and development that may have implications for deeper molecular insights into inflorescence and plant architecture in crops.
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Affiliation(s)
- Helmy M Youssef
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.,Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Kai Eggert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ravi Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ahmad M Alqudah
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Naser Poursarebani
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Arash Fazeli
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Ilam University, Ilam, Iran
| | - Shun Sakuma
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.,Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Akemi Tagiri
- National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Geetha Govind
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.,Reliance R&D Centre, Reliance Corporate Park, Ghansoli, Navi Mumbai, India
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Alnarp, Sweden
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences (NIAS), Tsukuba, Japan
| | - Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany.,International Rice Research Institute (IRRI), Grain Quality and Nutrition Center, Metro Manila, Philippines
| | - Thorsten Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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194
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Jia Q, Tan C, Wang J, Zhang XQ, Zhu J, Luo H, Yang J, Westcott S, Broughton S, Moody D, Li C. Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics 2016; 17:911. [PMID: 27835941 PMCID: PMC5106812 DOI: 10.1186/s12864-016-3247-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/02/2016] [Indexed: 12/04/2022] Open
Abstract
Background Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. .,Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China.
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hao Luo
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Sharon Westcott
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - David Moody
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
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195
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Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley. Sci Rep 2016; 6:36122. [PMID: 27786300 PMCID: PMC5081693 DOI: 10.1038/srep36122] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/11/2016] [Indexed: 12/12/2022] Open
Abstract
The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.
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196
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Hisano H, Tsujimura M, Yoshida H, Terachi T, Sato K. Mitochondrial genome sequences from wild and cultivated barley (Hordeum vulgare). BMC Genomics 2016; 17:824. [PMID: 27776481 PMCID: PMC5078923 DOI: 10.1186/s12864-016-3159-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Background Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulgare) have cross compatibility and closely related genomes, although a significant number of nucleotide polymorphisms have been reported between their genomes. Results We determined the complete nucleotide sequences of the mitochondrial genomes of wild and cultivated barley. Two independent circular maps of the 525,599 bp barley mitochondrial genome were constructed by de novo assembly of high-throughput sequencing reads of barley lines H602 and Haruna Nijo, with only three SNPs detected between haplotypes. These mitochondrial genomes contained 33 protein-coding genes, three ribosomal RNAs, 16 transfer RNAs, 188 new ORFs, six major repeat sequences and several types of transposable elements. Of the barley mitochondrial genome-encoded proteins, NAD6, NAD9 and RPS4 had unique structures among grass species. Conclusions The mitochondrial genome of barley was similar to those of other grass species in terms of gene content, but the configuration of the genes was highly differentiated from that of other grass species. Mitochondrial genome sequencing is essential for annotating the barley nuclear genome; our mitochondrial sequencing identified a significant number of fragmented mitochondrial sequences in the reported nuclear genome sequences. Little polymorphism was detected in the barley mitochondrial genome sequences, which should be explored further to elucidate the evolution of barley. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3159-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Mai Tsujimura
- Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Hideya Yoshida
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Toru Terachi
- Plant Organelle Genomics Research Center and Faculty of Life Sciences, Kyoto Sangyo University, Motoyama, Kamigamo, Kita-ku, Kyoto, 603-8555, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, 710-0046, Japan.
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197
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Smith AR, Zhao D. Sterility Caused by Floral Organ Degeneration and Abiotic Stresses in Arabidopsis and Cereal Grains. FRONTIERS IN PLANT SCIENCE 2016; 7:1503. [PMID: 27790226 PMCID: PMC5064672 DOI: 10.3389/fpls.2016.01503] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 09/21/2016] [Indexed: 05/18/2023]
Abstract
Natural floral organ degeneration or abortion results in unisexual or fully sterile flowers, while abiotic stresses lead to sterility after initiation of floral reproductive organs. Since normal flower development is essential for plant sexual reproduction and crop yield, it is imperative to have a better understanding of plant sterility under regular and stress conditions. Here, we review the functions of ABC genes together with their downstream genes in floral organ degeneration and the formation of unisexual flowers in Arabidopsis and several agriculturally significant cereal grains. We further explore the roles of hormones, including auxin, brassinosteroids, jasmonic acid, gibberellic acid, and ethylene, in floral organ formation and fertility. We show that alterations in genes affecting hormone biosynthesis, hormone transport and perception cause loss of stamens/carpels, abnormal floral organ development, poor pollen production, which consequently result in unisexual flowers and male/female sterility. Moreover, abiotic stresses, such as heat, cold, and drought, commonly affect floral organ development and fertility. Sterility is induced by abiotic stresses mostly in male floral organ development, particularly during meiosis, tapetum development, anthesis, dehiscence, and fertilization. A variety of genes including those involved in heat shock, hormone signaling, cold tolerance, metabolisms of starch and sucrose, meiosis, and tapetum development are essential for plants to maintain normal fertility under abiotic stress conditions. Further elucidation of cellular, biochemical, and molecular mechanisms about regulation of fertility will improve yield and quality for many agriculturally valuable crops.
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Affiliation(s)
| | - Dazhong Zhao
- Department of Biological Sciences, University of Wisconsin-Milwaukee, MilwaukeeWI, USA
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198
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Yang L, Yang CJ, Cheng Q, Xue W, Doebley JF. Mapping Prolificacy QTL in Maize and Teosinte. J Hered 2016; 107:674-678. [PMID: 27660498 DOI: 10.1093/jhered/esw064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/16/2016] [Indexed: 11/14/2022] Open
Abstract
Teosinte, the ancestor of maize, possesses multiple ears at each node along its main stalk, whereas maize has only a single ear at each node. With its greater ear number, teosinte is referred to as being more prolific. The grassy tillers 1 (gt1) gene has been identified as a large-effect quantitative trait locus underlying this prolificacy difference between maize and teosinte, and the causal polymorphism for the difference was mapped to a 2.7kb control region 5' of the gt1 ORF. The most common maize haplotype (M1) at the gt1 control region confers low prolificacy. A prior study reported that 29% of maize varieties possess the teosinte haplotype (T) for the control region, although these varieties are nonprolific. This observation suggested that these maize lines might possess an additional factor, other than gt1, suppressing prolificacy in maize. We discovered that the factor suppressing prolificacy in maize varieties with the gt1 T haplotype mapped to a 3.20 cM interval, which includes gt1 Subsequent DNA sequence analysis revealed that the maize varieties with the apparent T haplotype actually possess a distinct maize haplotype (M2) that is similar, but not identical, to the T haplotype in sequence but is associated with a nonprolific phenotype similar to the M1 haplotype. Our data indicate that the M2 haplotype or a closely linked factor confers a nonprolific phenotype. Our data suggest that 2 different alleles or haplotypes (M1 and M2) of gt1 were selected during domestication, and that nonprolificacy in all maize varieties is likely a result of allele substitutions at gt1.
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Affiliation(s)
- Liyan Yang
- From the Life Science College, Shanxi Normal University, No. 1 Gongyuan Street, Linfen City, Shanxi Province 041004, China (L. Yang) and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706 (C. J. Yang, Cheng, Xue, and Doebley)
| | - Chin Jian Yang
- From the Life Science College, Shanxi Normal University, No. 1 Gongyuan Street, Linfen City, Shanxi Province 041004, China (L. Yang) and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706 (C. J. Yang, Cheng, Xue, and Doebley)
| | - Qi Cheng
- From the Life Science College, Shanxi Normal University, No. 1 Gongyuan Street, Linfen City, Shanxi Province 041004, China (L. Yang) and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706 (C. J. Yang, Cheng, Xue, and Doebley)
| | - Wei Xue
- From the Life Science College, Shanxi Normal University, No. 1 Gongyuan Street, Linfen City, Shanxi Province 041004, China (L. Yang) and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706 (C. J. Yang, Cheng, Xue, and Doebley)
| | - John F Doebley
- From the Life Science College, Shanxi Normal University, No. 1 Gongyuan Street, Linfen City, Shanxi Province 041004, China (L. Yang) and Laboratory of Genetics, University of Wisconsin-Madison, 425 Henry Mall, Madison, WI 53706 (C. J. Yang, Cheng, Xue, and Doebley).
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199
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Genome-wide identification and characterization of the homeodomain-leucine zipper I family of genes in cotton ( Gossypium spp.). ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.plgene.2016.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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200
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Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation. Nat Genet 2016; 48:1024-30. [PMID: 27428750 DOI: 10.1038/ng.3612] [Citation(s) in RCA: 157] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 06/13/2016] [Indexed: 12/18/2022]
Abstract
After domestication, during a process of widespread range extension, barley adapted to a broad spectrum of agricultural environments. To explore how the barley genome responded to the environmental challenges it encountered, we sequenced the exomes of a collection of 267 georeferenced landraces and wild accessions. A combination of genome-wide analyses showed that patterns of variation have been strongly shaped by geography and that variant-by-environment associations for individual genes are prominent in our data set. We observed significant correlations of days to heading (flowering) and height with seasonal temperature and dryness variables in common garden experiments, suggesting that these traits were major drivers of environmental adaptation in the sampled germplasm. A detailed analysis of known flowering-associated genes showed that many contain extensive sequence variation and that patterns of single- and multiple-gene haplotypes exhibit strong geographical structuring. This variation appears to have substantially contributed to range-wide ecogeographical adaptation, but many factors key to regional success remain unidentified.
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