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Long Y, Wang C, Liu C, Li H, Pu A, Dong Z, Wei X, Wan X. Molecular mechanisms controlling grain size and weight and their biotechnological breeding applications in maize and other cereal crops. J Adv Res 2024; 62:27-46. [PMID: 37739122 PMCID: PMC11331183 DOI: 10.1016/j.jare.2023.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 09/03/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Cereal crops are a primary energy source for humans. Grain size and weight affect both evolutionary fitness and grain yield of cereals. Although studies on gene mining and molecular mechanisms controlling grain size and weight are constantly emerging in cereal crops, only a few systematic reviews on the underlying molecular mechanisms and their breeding applications are available so far. AIM OF REVIEW This review provides a general state-of-the-art overview of molecular mechanisms and targeted strategies for improving grain size and weight of cereals as well as insights for future yield-improving biotechnology-assisted breeding. KEY SCIENTIFIC CONCEPTS OF REVIEW In this review, the evolution of research on grain size and weight over the last 20 years is traced based on a bibliometric analysis of 1158 publications and the main signaling pathways and transcriptional factors involved are summarized. In addition, the roles of post-transcriptional regulation and photosynthetic product accumulation affecting grain size and weight in maize and rice are outlined. State-of-the-art strategies for discovering novel genes related to grain size and weight in maize and other cereal crops as well as advanced breeding biotechnology strategies being used for improving yield including marker-assisted selection, genomic selection, transgenic breeding, and genome editing are also discussed.
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Affiliation(s)
- Yan Long
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Cheng Wang
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Aqing Pu
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, University of Science and Technology Beijing, Beijing 100083, China; Industry Research Institute of Biotechnology Breeding, Yili Normal University, Yining 835000, China; Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China.
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Cosenza F, Shrestha A, Van Inghelandt D, Casale FA, Wu PY, Weisweiler M, Li J, Wespel F, Stich B. Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2385-2402. [PMID: 38330219 PMCID: PMC11016846 DOI: 10.1093/jxb/erae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 02/07/2024] [Indexed: 02/10/2024]
Abstract
Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.
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Affiliation(s)
- Francesco Cosenza
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Delphine Van Inghelandt
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Federico A Casale
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Po-Ya Wu
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Marius Weisweiler
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
| | - Franziska Wespel
- Saatzucht Josef Breun GmbH Co. KG, Amselweg 1, 91074 Herzogenaurach, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, 40225 Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, 50829 Köln, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany
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Kartseva T, Aleksandrov V, Alqudah AM, Arif MAR, Kocheva K, Doneva D, Prokopova K, Börner A, Misheva S. GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight. PLANTS (BASEL, SWITZERLAND) 2024; 13:1084. [PMID: 38674493 PMCID: PMC11054703 DOI: 10.3390/plants13081084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits-grain protein content (GPC) and thousand kernel weight (TKW)-across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.
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Affiliation(s)
- Tania Kartseva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Vladimir Aleksandrov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mian Abdur Rehman Arif
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan;
| | - Konstantina Kocheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Dilyana Doneva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Katelina Prokopova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), OT Gatersleben, Corrensstraße 3, 06466 Seeland, Germany;
| | - Svetlana Misheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
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Hansson M, Youssef HM, Zakhrabekova S, Stuart D, Svensson JT, Dockter C, Stein N, Waugh R, Lundqvist U, Franckowiak J. A guide to barley mutants. Hereditas 2024; 161:11. [PMID: 38454479 PMCID: PMC10921644 DOI: 10.1186/s41065-023-00304-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 11/24/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND Mutants have had a fundamental impact upon scientific and applied genetics. They have paved the way for the molecular and genomic era, and most of today's crop plants are derived from breeding programs involving mutagenic treatments. RESULTS Barley (Hordeum vulgare L.) is one of the most widely grown cereals in the world and has a long history as a crop plant. Barley breeding started more than 100 years ago and large breeding programs have collected and generated a wide range of natural and induced mutants, which often were deposited in genebanks around the world. In recent years, an increased interest in genetic diversity has brought many historic mutants into focus because the collections are regarded as valuable resources for understanding the genetic control of barley biology and barley breeding. The increased interest has been fueled also by recent advances in genomic research, which provided new tools and possibilities to analyze and reveal the genetic diversity of mutant collections. CONCLUSION Since detailed knowledge about phenotypic characters of the mutants is the key to success of genetic and genomic studies, we here provide a comprehensive description of mostly morphological barley mutants. The review is closely linked to the International Database for Barley Genes and Barley Genetic Stocks ( bgs.nordgen.org ) where further details and additional images of each mutant described in this review can be found.
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Affiliation(s)
- Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
| | - Helmy M Youssef
- Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
- Institute of Agricultural and Nutritional Sciences, Faculty of Natural Sciences III, Martin Luther University Halle-Wittenberg, Halle, 06120, Germany
| | | | - David Stuart
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | - Jan T Svensson
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, E06466, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Division of Plant Sciences, University of Dundee, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- School of Agriculture Food and Wine, Waite Campus, The University of Adelaide, Urrbrae, 5064, Australia
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Växthusvägen 12, 23456, Alnarp, Sweden
| | - Jerome Franckowiak
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, 411 Borlaug Hall, 1991 Upper Buford Circle, St Paul, MN, 55108, USA
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Pandey S. Agronomic potential of plant-specific Gγ proteins. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:337-347. [PMID: 38623166 PMCID: PMC11016034 DOI: 10.1007/s12298-024-01428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/17/2024] [Accepted: 02/28/2024] [Indexed: 04/17/2024]
Abstract
The vascular plant-specific type III Gγ proteins have emerged as important targets for biotechnological applications. These proteins are exemplified by Arabidopsis AGG3, rice Grain Size 3 (GS3), Dense and Erect Panicle 1 (DEP1), and GGC2 and regulate plant stature, seed size, weight and quality, nitrogen use efficiency, and multiple stress responses. These Gγ proteins are an integral component of the plant heterotrimeric G-protein complex and differ from the canonical Gγ proteins due to the presence of a long, cysteine-rich C-terminal region. Most cereal genomes encode three or more of these proteins, which have similar N-terminal Gγ domains but varying lengths of the C-terminal domain. The C-terminal domain is hypothesized to give specificity to the protein function. Intriguingly, many accessions of cultivated cereals have natural deletion of this region in one or more proteins, but the mechanistic details of protein function remain perplexing. Distinct, sometimes contrasting, effects of deletion of the C-terminal region have been reported in different crops or under varying environmental conditions. This review summarizes the known roles of type III Gγ proteins, the possible action mechanisms, and a perspective on what is needed to comprehend their full agronomic potential.
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Affiliation(s)
- Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132 USA
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6
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Lukina KA, Porotnikov IV, Antonova OY, Kovaleva ON. Determination of the Allelic Composition of the sdw1/denso ( HvGA20ox2), uzu1 ( HvBRI1) and ari-e ( HvDep1) Genes in Spring Barley Accessions from the VIR Collection. PLANTS (BASEL, SWITZERLAND) 2024; 13:376. [PMID: 38337909 PMCID: PMC10857314 DOI: 10.3390/plants13030376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 01/19/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
The lodging of barley significantly limits its potential yield, leads to the deterioration of grain quality, and complicates mechanized harvesting. More than 30 dwarfness and semi-dwarfness genes and loci are known for barley, and their involvement in breeding can solve the problem of lodging. The most common dwarfing alleles are of the genes sdw1/denso (HvGA20ox2), uzu1 (HvBRI1), and ari-e (HvDep1). The aim of this study was the design of dCAPS markers for the sdw1.c and ari-e.GP alleles and the molecular screening of barley accessions from the VIR collection for identifying these and other dwarfing alleles commonly used in breeding. Two dCAPS markers have been developed to identify the sdw1.c allele of the HvGA20ox2 gene and ari-e.GP of HvDep1. These dCAPS markers and two known from the literature CAPS and dCAPS markers of the alleles sdw1.a/sdw1.e, sdw1.c, sdw1.d, and uzu1.a were used in the molecular screening of 32 height-contrasting barley accessions. This made it possible to identify the accessions with alleles sdw1.a/sdw1.e, sdw1.c, and sdw1.d of the HvGA20ox2 gene, as well as accessions with a combination of sdw1.c and uzu1.a alleles of the genes HvGA20ox2 and HvBRI1. A comparison of the results of genotyping and phenotyping showed that the presence of dwarfing alleles in all genotypes determines high or medium lodging resistance regardless of the influence of weather conditions. Twelve accessions were found to contain the new allele sdw1.ins of the HvGA20ox2 gene, which differs from the known allele sdw1.c by a larger size of PCR products. It is characterized by the Thalos_2 transposon insertion; the subsequent GTTA insertion, common with the sdw1.c allele; and by a single-nucleotide G→A substitution at the 165 position.
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Affiliation(s)
- Kseniia A. Lukina
- Federal Research Center N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg 190031, Russia; (I.V.P.); (O.Y.A.); (O.N.K.)
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7
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Schreiber M, Wonneberger R, Haaning AM, Coulter M, Russell J, Himmelbach A, Fiebig A, Muehlbauer GJ, Stein N, Waugh R. Genomic resources for a historical collection of cultivated two-row European spring barley genotypes. Sci Data 2024; 11:66. [PMID: 38216606 PMCID: PMC10786862 DOI: 10.1038/s41597-023-02850-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 12/12/2023] [Indexed: 01/14/2024] Open
Abstract
Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.
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Affiliation(s)
- Miriam Schreiber
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Ronja Wonneberger
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Allison M Haaning
- Department of Agronomy and Plant Genetics, The University of Minnesota, St. Paul, MN, 55108, USA
| | - Max Coulter
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Anne Fiebig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, The University of Minnesota, St. Paul, MN, 55108, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK.
- Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK.
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Desta KT, Choi YM, Yoon H, Lee S, Yi J, Jeon YA, Wang X, Park JC, Kim KM, Shin MJ. Comprehensive Characterization of Global Barley ( Hordeum vulgare L.) Collection Using Agronomic Traits, β-Glucan Level, Phenolic Content, and Antioxidant Activities. PLANTS (BASEL, SWITZERLAND) 2024; 13:169. [PMID: 38256723 PMCID: PMC10818635 DOI: 10.3390/plants13020169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/18/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
This study characterized the diversity of 367 barley collections from 27 different countries, including 5 control cultivars, using several phenotypic traits. Morphological traits, including spike type, grain morphology, cold damage, and lodging rate, exhibited wide variations. Eighteen accessions matured early, while four accessions had longer culm and spike lengths than the controls. The ranges of total phenolic content (TPC), β-glucan content, ABTS•+ scavenging activity, DPPH• scavenging activity, and reducing power (RP) were 1.79-6.79 mg GAE/g, 0.14-8.41 g/100 g, 3.07-13.54 mg AAE/100 g, 1.56-6.24 mg AAE/g, and 1.31-7.86 mg AAE/g, respectively. Betaone, one of the controls, had the highest β-glucan content. Two accessions had β-glucan levels close to Betaone. Furthermore, 20 accessions exhibited increased TPC compared to the controls, while 5 accessions displayed elevated ABTS•+ scavenging activity. Among these, one accession also exhibited higher DPPH• scavenging activity and RP simultaneously. Based on the statistical analysis of variance, all the quantitative traits were significantly affected by the difference in origin (p < 0.05). On the other hand, grain morphology significantly affected biochemical traits. Multivariate analysis classified barley accessions into eight groups, demonstrating variations in quantitative traits. There were noteworthy correlations between biochemical and agronomical traits. Overall, this study characterized several barley varieties of different origins, anticipating future genomic research. The barley accessions with superior performances could be valuable alternatives in breeding.
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Affiliation(s)
- Kebede Taye Desta
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Yu-Mi Choi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Hyemyeong Yoon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sukyeung Lee
- International Technology Cooperation Center, Technology Cooperation Bureau, Rural Development Administration, Jeonju 54875, Republic of Korea
| | - Jungyoon Yi
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Young-ah Jeon
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Xiaohan Wang
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jin-Cheon Park
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Kyeong-Min Kim
- National Institute of Crop Science, Rural Development Administration, Wanju 55365, Republic of Korea
| | - Myoung-Jae Shin
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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9
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Mohanasundaram B, Pandey S. Moving beyond the arabidopsis-centric view of G-protein signaling in plants. TRENDS IN PLANT SCIENCE 2023; 28:1406-1421. [PMID: 37625950 DOI: 10.1016/j.tplants.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 07/24/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Heterotrimeric G-protein-mediated signaling is a key mechanism to transduce a multitude of endogenous and environmental signals in diverse organisms. The scope and expectations of plant G-protein research were set by pioneering work in metazoans. Given the similarity of the core constituents, G-protein-signaling mechanisms were presumed to be universally conserved. However, because of the enormous diversity of survival strategies and endless forms among eukaryotes, the signal, its interpretation, and responses vary even among different plant groups. Earlier G-protein research in arabidopsis (Arabidopsis thaliana) has emphasized its divergence from Metazoa. Here, we compare recent evidence from diverse plant lineages with the available arabidopsis G-protein model and discuss the conserved and novel protein components, signaling mechanisms, and response regulation.
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Affiliation(s)
| | - Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St Louis, MO 63132, USA.
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10
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Gasparis S, Miłoszewski MM. Genetic Basis of Grain Size and Weight in Rice, Wheat, and Barley. Int J Mol Sci 2023; 24:16921. [PMID: 38069243 PMCID: PMC10706642 DOI: 10.3390/ijms242316921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/27/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Grain size is a key component of grain yield in cereals. It is a complex quantitative trait controlled by multiple genes. Grain size is determined via several factors in different plant development stages, beginning with early tillering, spikelet formation, and assimilates accumulation during the pre-anthesis phase, up to grain filling and maturation. Understanding the genetic and molecular mechanisms that control grain size is a prerequisite for improving grain yield potential. The last decade has brought significant progress in genomic studies of grain size control. Several genes underlying grain size and weight were identified and characterized in rice, which is a model plant for cereal crops. A molecular function analysis revealed most genes are involved in different cell signaling pathways, including phytohormone signaling, transcriptional regulation, ubiquitin-proteasome pathway, and other physiological processes. Compared to rice, the genetic background of grain size in other important cereal crops, such as wheat and barley, remains largely unexplored. However, the high level of conservation of genomic structure and sequences between closely related cereal crops should facilitate the identification of functional orthologs in other species. This review provides a comprehensive overview of the genetic and molecular bases of grain size and weight in wheat, barley, and rice, focusing on the latest discoveries in the field. We also present possibly the most updated list of experimentally validated genes that have a strong effect on grain size and discuss their molecular function.
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Affiliation(s)
- Sebastian Gasparis
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland;
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11
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Torres Rodríguez MD, Bhatnagar N, Pandey S. Overexpression of a Plant-Specific Gγ Protein, AGG3, in the Model Monocot Setaria viridis Confers Tolerance to Heat Stress. PLANT & CELL PHYSIOLOGY 2023; 64:1243-1256. [PMID: 37572092 DOI: 10.1093/pcp/pcad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/14/2023] [Accepted: 08/10/2023] [Indexed: 08/14/2023]
Abstract
The vascular plant-specific, cysteine-rich type III Gγ proteins, which are integral components of the heterotrimeric G-protein complex, play crucial roles in regulating a multitude of plant processes, including those related to crop yield and responses to abiotic stresses. The presence of multiple copies of type III Gγ proteins in most plants and a propensity of the presence of specific truncated alleles in many cultivated crops present an ambiguous picture of their roles in modulating specific responses. AGG3 is a canonical type III Gγ protein of Arabidopsis, and its overexpression in additional model crops offers the opportunity to directly evaluate the effects of protein expression levels on plant phenotypes. We have shown that AGG3 overexpression in the monocot model Setaria viridis leads to an increase in seed yield. In this study, we have investigated the response of the S. viridis plants overexpressing AGG3 to heat stress (HS), one of the most important abiotic stresses affecting crops worldwide. We show that a short span of HS at a crucial developmental time point has a significant effect on plant yield in the later stages. We also show that plants with higher levels of AGG3 are more tolerant to HS. This is attributed to an altered regulation of stress-responsive genes and improved modulation of the photosynthetic efficiency during the stress. Overall, our results confirm that AGG3 plays a crucial role in regulating plant responses to unfavorable environmental conditions and may contribute positively to avoiding crop yield losses.
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Affiliation(s)
| | - Nikita Bhatnagar
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
| | - Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO 63132, USA
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12
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Rozanova IV, Grigoriev YN, Efimov VM, Igoshin AV, Khlestkina EK. Genetic Dissection of Spike Productivity Traits in the Siberian Collection of Spring Barley. Biomolecules 2023; 13:909. [PMID: 37371489 DOI: 10.3390/biom13060909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
Barley (Hordeum vulgare L.) is one of the most commonly cultivated cereals worldwide. Its local varieties can represent a valuable source of unique genetic variants useful for crop improvement. The aim of this study was to reveal loci contributing to spike productivity traits in Siberian spring barley and to develop diagnostic DNA markers for marker-assisted breeding programs. For this purpose we conducted a genome-wide association study using a panel of 94 barley varieties. In total, 64 SNPs significantly associated with productivity traits were revealed. Twenty-three SNP markers were validated by genotyping in an independent sample set using competitive allele-specific PCR (KASP). Finally, fourteen markers associated with spike productivity traits on chromosomes 2H, 4H and 5H can be suggested for use in breeding programs.
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Affiliation(s)
- Irina V Rozanova
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Yuriy N Grigoriev
- Siberian Research Institute of Plant Cultivation and Breeding-Branch of Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Krasnoobsk, 630501 Novosibirsk, Russia
| | - Vadim M Efimov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Alexander V Igoshin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
| | - Elena K Khlestkina
- N.I. Vavilov All-Russian Research Institute of Plant Genetic Resources (VIR), 190000 St. Petersburg, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrentjeva Ave. 10, 630090 Novosibirsk, Russia
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13
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Hong Y, Zhang M, Xu R. Genetic Localization and Homologous Genes Mining for Barley Grain Size. Int J Mol Sci 2023; 24:ijms24054932. [PMID: 36902360 PMCID: PMC10003025 DOI: 10.3390/ijms24054932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 03/08/2023] Open
Abstract
Grain size is an important agronomic trait determining barley yield and quality. An increasing number of QTLs (quantitative trait loci) for grain size have been reported due to the improvement in genome sequencing and mapping. Elucidating the molecular mechanisms underpinning barley grain size is vital for producing elite cultivars and accelerating breeding processes. In this review, we summarize the achievements in the molecular mapping of barley grain size over the past two decades, highlighting the results of QTL linkage analysis and genome-wide association studies. We discuss the QTL hotspots and predict candidate genes in detail. Moreover, reported homologs that determine the seed size clustered into several signaling pathways in model plants are also listed, providing the theoretical basis for mining genetic resources and regulatory networks of barley grain size.
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Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225127, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou 225127, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225127, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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14
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Zhang A, Zhao T, Hu X, Zhou Y, An Y, Pei H, Sun D, Sun G, Li C, Ren X. Identification of QTL underlying the main stem related traits in a doubled haploid barley population. FRONTIERS IN PLANT SCIENCE 2022; 13:1063988. [PMID: 36531346 PMCID: PMC9751491 DOI: 10.3389/fpls.2022.1063988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/14/2022] [Indexed: 06/17/2023]
Abstract
Lodging reduces grain yield in cereal crops. The height, diameter and strength of stem are crucial for lodging resistance, grain yield, and photosynthate transport in barley. Understanding the genetic basis of stem benefits barley breeding. Here, we evaluated 13 stem related traits after 28 days of heading in a barley DH population in two consecutive years. Significant phenotypic correlations between lodging index (LI) and other stem traits were observed. Three mapping methods using the experimental data and the BLUP data, detected 27 stable and major QTLs, and 22 QTL clustered regions. Many QTLs were consistent with previously reported traits for grain filling rate, internodes, panicle and lodging resistance. Further, candidate genes were predicted for stable and major QTLs and were associated with plant development and adverse stress in the transition from vegetative stage to reproductive stage. This study provided potential genetic basis and new information for exploring barley stem morphology, and laid a foundation for map-based cloning and further fine mapping of these QTLs.
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Affiliation(s)
- Anyong Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Ting Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xue Hu
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yu Zhou
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yue An
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Haiyi Pei
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | - Chengdao Li
- College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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15
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Luo G, Najafi J, Correia PMP, Trinh MDL, Chapman EA, Østerberg JT, Thomsen HC, Pedas PR, Larson S, Gao C, Poland J, Knudsen S, DeHaan L, Palmgren M. Accelerated Domestication of New Crops: Yield is Key. PLANT & CELL PHYSIOLOGY 2022; 63:1624-1640. [PMID: 35583202 PMCID: PMC9680862 DOI: 10.1093/pcp/pcac065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 04/17/2022] [Accepted: 05/17/2022] [Indexed: 05/05/2023]
Abstract
Sustainable agriculture in the future will depend on crops that are tolerant to biotic and abiotic stresses, require minimal input of water and nutrients and can be cultivated with a minimal carbon footprint. Wild plants that fulfill these requirements abound in nature but are typically low yielding. Thus, replacing current high-yielding crops with less productive but resilient species will require the intractable trade-off of increasing land area under cultivation to produce the same yield. Cultivating more land reduces natural resources, reduces biodiversity and increases our carbon footprint. Sustainable intensification can be achieved by increasing the yield of underutilized or wild plant species that are already resilient, but achieving this goal by conventional breeding programs may be a long-term prospect. De novo domestication of orphan or crop wild relatives using mutagenesis is an alternative and fast approach to achieve resilient crops with high yields. With new precise molecular techniques, it should be possible to reach economically sustainable yields in a much shorter period of time than ever before in the history of agriculture.
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Affiliation(s)
- Guangbin Luo
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Javad Najafi
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Pedro M P Correia
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Mai Duy Luu Trinh
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
| | - Elizabeth A Chapman
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | | | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Steve Larson
- US Department of Agriculture (USDA), USDA–ARS Forage & Range Research Lab, Utah State University Logan, Logan, UT 84322, USA
| | - Caixia Gao
- Center for Genome Editing, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jesse Poland
- Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal, Makkah 23955, Saudi Arabia
| | - Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, Copenhagen V DK-1799, Denmark
| | - Lee DeHaan
- The Land Institute, Salina, KS 67401, USA
| | - Michael Palmgren
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, Frederiksberg C DK-1871, Denmark
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16
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Knudsen S, Wendt T, Dockter C, Thomsen HC, Rasmussen M, Egevang Jørgensen M, Lu Q, Voss C, Murozuka E, Østerberg JT, Harholt J, Braumann I, Cuesta-Seijo JA, Kale SM, Bodevin S, Tang Petersen L, Carciofi M, Pedas PR, Opstrup Husum J, Nielsen MTS, Nielsen K, Jensen MK, Møller LA, Gojkovic Z, Striebeck A, Lengeler K, Fennessy RT, Katz M, Garcia Sanchez R, Solodovnikova N, Förster J, Olsen O, Møller BL, Fincher GB, Skadhauge B. FIND-IT: Accelerated trait development for a green evolution. SCIENCE ADVANCES 2022; 8:eabq2266. [PMID: 36001660 PMCID: PMC9401622 DOI: 10.1126/sciadv.abq2266] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/13/2022] [Indexed: 06/15/2023]
Abstract
Improved agricultural and industrial production organisms are required to meet the future global food demands and minimize the effects of climate change. A new resource for crop and microbe improvement, designated FIND-IT (Fast Identification of Nucleotide variants by droplet DigITal PCR), provides ultrafast identification and isolation of predetermined, targeted genetic variants in a screening cycle of less than 10 days. Using large-scale sample pooling in combination with droplet digital PCR (ddPCR) greatly increases the size of low-mutation density and screenable variant libraries and the probability of identifying the variant of interest. The method is validated by screening variant libraries totaling 500,000 barley (Hordeum vulgare) individuals and isolating more than 125 targeted barley gene knockout lines and miRNA or promoter variants enabling functional gene analysis. FIND-IT variants are directly applicable to elite breeding pipelines and minimize time-consuming technical steps to accelerate the evolution of germplasm.
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Affiliation(s)
- Søren Knudsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Toni Wendt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Magnus Rasmussen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Qiongxian Lu
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Cynthia Voss
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Emiko Murozuka
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jesper Harholt
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ilka Braumann
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jose A. Cuesta-Seijo
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sandip M. Kale
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sabrina Bodevin
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lise Tang Petersen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Pai Rosager Pedas
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Jeppe Opstrup Husum
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Kasper Nielsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Mikkel K. Jensen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Lillian Ambus Møller
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Zoran Gojkovic
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Alexander Striebeck
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Klaus Lengeler
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ross T. Fennessy
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Michael Katz
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Rosa Garcia Sanchez
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | | | - Jochen Förster
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Ole Olsen
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Centre for Synthetic Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Geoffrey B. Fincher
- Australian Research Council Centre of Excellence in Plant Cell Walls School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
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17
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Mohanasundaram B, Dodds A, Kukshal V, Jez JM, Pandey S. Distribution and the evolutionary history of G-protein components in plant and algal lineages. PLANT PHYSIOLOGY 2022; 189:1519-1535. [PMID: 35377452 PMCID: PMC9237705 DOI: 10.1093/plphys/kiac153] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 03/08/2022] [Indexed: 05/25/2023]
Abstract
Heterotrimeric G-protein complexes comprising Gα-, Gβ-, and Gγ-subunits and the regulator of G-protein signaling (RGS) are conserved across most eukaryotic lineages. Signaling pathways mediated by these proteins influence overall growth, development, and physiology. In plants, this protein complex has been characterized primarily from angiosperms with the exception of spreading-leaved earth moss (Physcomitrium patens) and Chara braunii (charophytic algae). Even within angiosperms, specific G-protein components are missing in certain species, whereas unique plant-specific variants-the extra-large Gα (XLGα) and the cysteine-rich Gγ proteins-also exist. The distribution and evolutionary history of G-proteins and their function in nonangiosperm lineages remain mostly unknown. We explored this using the wealth of available sequence data spanning algae to angiosperms representing extant species that diverged approximately 1,500 million years ago, using BLAST, synteny analysis, and custom-built Hidden Markov Model profile searches. We show that a minimal set of components forming the XLGαβγ trimer exists in the entire land plant lineage, but their presence is sporadic in algae. Additionally, individual components have distinct evolutionary histories. The XLGα exhibits many lineage-specific gene duplications, whereas Gα and RGS show several instances of gene loss. Similarly, Gβ remained constant in both number and structure, but Gγ diverged before the emergence of land plants and underwent changes in protein domains, which led to three distinct subtypes. These results highlight the evolutionary oddities and summarize the phyletic patterns of this conserved signaling pathway in plants. They also provide a framework to formulate pertinent questions on plant G-protein signaling within an evolutionary context.
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Affiliation(s)
| | - Audrey Dodds
- Donald Danforth Plant Science Center, St Louis, Missouri 63132, USA
| | - Vandna Kukshal
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
| | - Joseph M Jez
- Department of Biology, Washington University, St Louis, Missouri 63130, USA
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18
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Hanak T, Madsen CK, Brinch-Pedersen H. Genome Editing-accelerated Re-Domestication (GEaReD) - a new major direction in plant breeding. Biotechnol J 2022; 17:e2100545. [PMID: 35120401 DOI: 10.1002/biot.202100545] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND The effects of climate change, soil depletion, a growing world population putting pressure on food safety and security are major challenges for agriculture in the 21st century. The breeding success of the green revolution has decelerated and current programs can only offset the yield affecting factors. PURPOSE AND SCOPE New approaches are urgently needed and we propose "Genome Editing-accelerated Re-Domestication" (GEaReD) as a major new direction in plant breeding. By combining the upcoming technologies for phenotyping, omics, and artificial intelligence with the promising new CRISPR-toolkits, this approach is closer than ever. SUMMARY AND CONCLUSION Wild relatives of current crops are often adapted to harsh environments and have a high genetic diversity. Redomestication of wild barley or teosinte could generate new cultivars adapted to environmental changes. De novo domestication of perennial relatives such as Hordeum bulbosum could counter soil depletion and increase soil carbon. Recent research already proved the principle of redomestication in tomato and rice and therefore laid the foundation for GEaReD. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tobias Hanak
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
| | - Claus Krogh Madsen
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
| | - Henrik Brinch-Pedersen
- Department of Agroecology, Aarhus University, Crop Genetics and Biotechnology Forsøgsvej 1, Slagelse, 4200, Denmark
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19
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Kong D, Xu J, Wang L, Wang H, You E, Li X, Chen T, Shen Y. Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai-Tibetan Plateau. FRONTIERS IN PLANT SCIENCE 2022; 13:822607. [PMID: 35185989 PMCID: PMC8847792 DOI: 10.3389/fpls.2022.822607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size.
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Affiliation(s)
- Doudou Kong
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xiaolan Li
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Laboratory for Research and Utilization of Qinghai-Tibetan Plateau Germplasm Resources, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, China
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20
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Sayre-Chavez B, Bettenhausen H, Windes S, Aron P, Cistué L, Fisk S, Helgerson L, Heuberger AL, Tynan S, Hayes P, Muñoz-Amatriaín M. Genetic basis of barley contributions to beer flavor. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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21
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Karunarathne SD, Han Y, Zhang XQ, Dang VH, Angessa TT, Li C. Using chlorate as an analogue to nitrate to identify candidate genes for nitrogen use efficiency in barley. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:47. [PMID: 37309383 PMCID: PMC10236044 DOI: 10.1007/s11032-021-01239-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/22/2021] [Indexed: 06/14/2023]
Abstract
Nitrogen (N) is one of the most important macronutrients for crop growth and development. Large amounts of N fertilizers are applied exogenously to improve grain yield and quality, which has led to environmental pollution and high cost of production. Therefore, improvement of N use efficiency (NUE) is a very important aspect for sustainable agriculture. Here, a pilot experiment was firstly conducted with a set of barley genotypes with confirmed NUE to validate the fast NUE screening, using chlorate as an analogue to nitrate. High NUE genotypes were susceptible to chlorate-induced toxicity whereas the low NUE genotypes were tolerant. A total of 180 barley RILs derived from four parents (Compass, GrangeR, Lockyer and La Trobe) were further screened for NUE. Leaf chlorosis induced by chlorate toxicity was the key parameter observed which was later related to low-N tolerance of the RILs. There was a distinct variation in chlorate susceptibility of the RILs with leaf chlorosis in the oldest leaf ranging from 10 to 80%. A genome-wide association study (GWAS) identified 9 significant marker-trait associations (MTAs) conferring high chlorate sensitivity on chromosomes 2H (2), 3H (1), 4H (4), 5H (1) and Un (1). Genes flanking with these markers were retrieved as potential targets for genetic improvement of NUE. Genes encoding Ferredoxin 3, leucine-rich receptor-like protein kinase family protein and receptor kinase are responsive to N stress. MTA4H5468 which exhibits concordance with high NUE phenotype can further be explored under different genetic backgrounds and successfully applied in marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01239-8.
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Affiliation(s)
- Sakura D. Karunarathne
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
| | - Yong Han
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151 Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
| | - Viet Hoang Dang
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150 Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA 6150 Australia
- Department of Primary Industries and Regional Development, 3 Baron-Hay Court, South Perth, WA 6151 Australia
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22
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Lu Q, Dockter C, Sirijovski N, Zakhrabekova S, Lundqvist U, Gregersen PL, Hansson M. Analysis of barley mutants ert-c.1 and ert-d.7 reveals two loci with additive effect on plant architecture. PLANTA 2021; 254:9. [PMID: 34148131 PMCID: PMC8215040 DOI: 10.1007/s00425-021-03653-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/29/2021] [Indexed: 05/31/2023]
Abstract
Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-c Ert-d double mutant. Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.
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Affiliation(s)
- Qiongxian Lu
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J.C. Jacobsens Gade 4, 1799, Copenhagen V, Denmark
| | - Nick Sirijovski
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden
| | | | - Udda Lundqvist
- Nordic Genetic Resource Centre (NordGen), Smedjevägen 3, 23053, Alnarp, Sweden
| | - Per L Gregersen
- Department of Molecular Biology and Genetics, Aarhus University, Forsøgsvej 1, 4200, Slagelse, Denmark
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, 22362, Lund, Sweden.
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23
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Wang J, Wu X, Yue W, Zhao C, Yang J, Zhou M. Identification of QTL for barley grain size. PeerJ 2021; 9:e11287. [PMID: 33986999 PMCID: PMC8088763 DOI: 10.7717/peerj.11287] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/25/2021] [Indexed: 01/22/2023] Open
Abstract
Background Barley grain size is one of the key factors determining storage capacity during grain filling. Large, well-filled grains also have a high malt extract potential. Grain size is a complex quantitative trait and can be easily affected by environmental factors thus the identification of genes controlling the trait and the use of molecular markers linked to the genes in breeding program is the most effective way of improving grain size. Methods Grain sizes of 188 doubled-haploid (DH) lines derived from the cross of a Japanese malting barley variety (Naso Nijo) and a Chinese feed barley variety (TX9425) were obtained from three different sites in two consecutive years. The average data were used for identifying QTL for grain size. Results A total of four significant QTL were identified for grain length (GL) and three for grain width (GW). The two major GL QTL are located at similar positions to the QTL for malt extract on 2H and uzu gene on 3H, respectively. However, the GL QTL on 2H is more likely a different one from the malt extract QTL as most of the candidate genes are located outside the fine mapped QTL region for malt extract. The GL QTL on 3H is closely linked with uzu gene but not due to a pleiotropic effect of uzu. The three QTL for grain width on 1H, 2H and 5H, respectively, were located at same position to those for GL.
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Affiliation(s)
- Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaojian Wu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Wenhao Yue
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS, Australia
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24
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Thiel J, Koppolu R, Trautewig C, Hertig C, Kale SM, Erbe S, Mascher M, Himmelbach A, Rutten T, Esteban E, Pasha A, Kumlehn J, Provart NJ, Vanderauwera S, Frohberg C, Schnurbusch T. Transcriptional landscapes of floral meristems in barley. SCIENCE ADVANCES 2021; 7:eabf0832. [PMID: 33910893 PMCID: PMC8081368 DOI: 10.1126/sciadv.abf0832] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 02/26/2021] [Indexed: 05/02/2023]
Abstract
Organ development in plants predominantly occurs postembryonically through combinatorial activity of meristems; therefore, meristem and organ fate are intimately connected. Inflorescence morphogenesis in grasses (Poaceae) is complex and relies on a specialized floral meristem, called spikelet meristem, that gives rise to all other floral organs and ultimately the grain. The fate of the spikelet determines reproductive success and contributes toward yield-related traits in cereal crops. Here, we examined the transcriptional landscapes of floral meristems in the temperate crop barley (Hordeum vulgare L.) using RNA-seq of laser capture microdissected tissues from immature, developing floral structures. Our unbiased, high-resolution approach revealed fundamental regulatory networks, previously unknown pathways, and key regulators of barley floral fate and will equally be indispensable for comparative transcriptional studies of grass meristems.
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Affiliation(s)
- J Thiel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - R Koppolu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
| | - C Trautewig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - C Hertig
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S M Kale
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - S Erbe
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - M Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - A Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - T Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - E Esteban
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - A Pasha
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - J Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany
| | - N J Provart
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - S Vanderauwera
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - C Frohberg
- BASF Belgium Coordination Center CommV, Innovation Center Gent, Technologiepark-Zwijnaarde 101, 9052 Gent, Belgium
| | - T Schnurbusch
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
- Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany
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25
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Hong SY, Sun B, Straub D, Blaakmeer A, Mineri L, Koch J, Brinch-Pedersen H, Holme IB, Burow M, Lyngs Jørgensen HJ, Albà MM, Wenkel S. Heterologous microProtein expression identifies LITTLE NINJA, a dominant regulator of jasmonic acid signaling. Proc Natl Acad Sci U S A 2020; 117:26197-26205. [PMID: 33033229 PMCID: PMC7584889 DOI: 10.1073/pnas.2005198117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
MicroProteins are small, often single-domain proteins that are sequence-related to larger, often multidomain proteins. Here, we used a combination of comparative genomics and heterologous synthetic misexpression to isolate functional cereal microProtein regulators. Our approach identified LITTLE NINJA (LNJ), a microProtein that acts as a modulator of jasmonic acid (JA) signaling. Ectopic expression of LNJ in Arabidopsis resulted in stunted plants that resembled the decuple JAZ (jazD) mutant. In fact, comparing the transcriptomes of transgenic LNJ overexpressor plants and jazD revealed a large overlap of deregulated genes, suggesting that ectopic LNJ expression altered JA signaling. Transgenic Brachypodium plants with elevated LNJ expression levels showed deregulation of JA signaling as well and displayed reduced growth and enhanced production of side shoots (tiller). This tillering effect was transferable between grass species, and overexpression of LNJ in barley and rice caused similar traits. We used a clustered regularly interspaced short palindromic repeats (CRISPR) approach and created a LNJ-like protein in Arabidopsis by deleting parts of the coding sentence of the AFP2 gene that encodes a NINJA-domain protein. These afp2-crispr mutants were also stunted in size and resembled jazD Thus, similar genome-engineering approaches can be exploited as a future tool to create LNJ proteins and produce cereals with altered architectures.
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Affiliation(s)
- Shin-Young Hong
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Bin Sun
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
- NovoCrops Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Daniel Straub
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Anko Blaakmeer
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Lorenzo Mineri
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Department of Agricultural and Environmental Sciences, University of Milan, 20133 Milan, Italy
| | - Jonas Koch
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Henrik Brinch-Pedersen
- NovoCrops Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark
| | - Inger B Holme
- Department of Molecular Biology and Genetics, Research Centre Flakkebjerg, Aarhus University, 4200 Slagelse, Denmark
| | - Meike Burow
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
- DynaMo Centre of Excellence, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Research Institute, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies, 08003 Barcelona, Spain
| | - Stephan Wenkel
- Department of Plant and Environmental Sciences, University of Copenhagen, 1871 Frederiksberg C, Denmark;
- Copenhagen Plant Science Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
- NovoCrops Centre, University of Copenhagen, 1871 Frederiksberg C, Denmark
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26
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Watt C, Zhou G, McFawn LA, Li C. Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2095-2103. [PMID: 32193568 DOI: 10.1007/s00122-00020-03579-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/12/2020] [Indexed: 05/23/2023]
Abstract
A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Department of Primary Industry and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.
- Department of Primary Industry and Regional Development, South Perth, WA, Australia.
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27
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Watt C, Zhou G, McFawn LA, Li C. Fine mapping qGL2H, a major locus controlling grain length in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2095-2103. [PMID: 32193568 PMCID: PMC7311499 DOI: 10.1007/s00122-020-03579-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 03/12/2020] [Indexed: 05/08/2023]
Abstract
A major grain length QTL on chromosome 2H was fine mapped to a 140.9 Kb region containing three genes. Increasing yield is an important target for barley breeding programs. One approach to increase yield is by enhancing individual grain weights through the regulation of grain size. Fine mapping major grain size-related quantitative trait loci is necessary for future marker-assisted selection strategies, yet studies of this nature are limited in barley. In the present study, we utilised a doubled haploid population derived from two Australian malt barley varieties, Vlamingh and Buloke, coupled with extensive genotypic and phenotypic data from three independent environments. A major grain length locus identified on chromosome 2H designated qGL2H was fine mapped to a 140.9 Kb interval. qGL2H was able to account for 25.4% of the phenotypic variation for grain length and 10.2% for grain yield. Underlying qGL2H were three high-confidence predicted genes. One of these genes encodes a MYB transcription factor and represents a promising candidate for further genetic research.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia
- Department of Primary Industry and Regional Development, South Perth, WA, Australia
| | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Murdoch, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch, WA, Australia.
- Department of Primary Industry and Regional Development, South Perth, WA, Australia.
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28
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Exploring the Brassinosteroid Signaling in Monocots Reveals Novel Components of the Pathway and Implications for Plant Breeding. Int J Mol Sci 2020; 21:ijms21010354. [PMID: 31948086 PMCID: PMC6982108 DOI: 10.3390/ijms21010354] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/28/2019] [Accepted: 01/03/2020] [Indexed: 01/30/2023] Open
Abstract
Brassinosteroids (BRs) are a class of steroidal phytohormones which are key regulators of diverse processes during whole life cycle of plants. Studies conducted in the dicot model species Arabidopsis thaliana have allowed identification and characterization of various components of the BR signaling. It is currently known that the BR signaling is interconnected at various stages with other phytohormonal and stress signaling pathways. It enables a rapid and efficient adaptation of plant metabolism to constantly changing environmental conditions. However, our knowledge about mechanism of the BR signaling in the monocot species is rather limited. Thus, identification of new components of the BR signaling in monocots, including cereals, is an ongoing process and has already led to identification of some monocot-specific components of the BR signaling. It is of great importance as disturbances in the BR signaling influence architecture of mutant plants, and as a consequence, the reaction to environmental conditions. Currently, the modulation of the BR signaling is considered as a target to enhance yield and stress tolerance in cereals, which is of particular importance in the face of global climate change.
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29
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Hua W, Tan C, Xie J, Zhu J, Shang Y, Yang J, Zhang XQ, Wu X, Wang J, Li C. Alternative splicing of a barley gene results in an excess-tillering and semi-dwarf mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:163-177. [PMID: 31690990 DOI: 10.1007/s00122-019-03448-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/24/2019] [Indexed: 06/10/2023]
Abstract
An excess-tillering semi-dwarf gene Hvhtd was identified from an EMS-induced mutant in barley and alternative splicing results in excess-tillering semi-dwarf traits. Tillering and plant height are important traits determining plant architecture and grain production in cereal crops. This study identified an excess-tillering semi-dwarf mutant (htd) from an EMS-treated barley population. Genetic analysis of the F1, F2, and F2:3 populations showed that a single recessive gene controlled the excess-tillering semi-dwarf in htd. Using BSR-Seq and gene mapping, the Hvhtd gene was delimited within a 1.8 Mb interval on chromosome 2HL. Alignment of the RNA-Seq data with the functional genes in the interval identified a gene HORVU2Hr1G098820 with alternative splicing between exon2 and exon3 in the mutant, due to a G to A single-nucleotide substitution at the exon and intron junction. An independent mutant with a similar phenotype confirmed the result, with alternative splicing between exon3 and exon4. In both cases, the alternative splicing resulted in a non-functional protein. And the gene HORVU2Hr1G098820 encodes a trypsin family protein and may be involved in the IAA signaling pathway and differs from the mechanism of Green Revolution genes in the gibberellic acid metabolic pathway.
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Affiliation(s)
- Wei Hua
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinghuan Zhu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Yi Shang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Jianming Yang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Xiaojian Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junmei Wang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
- Department of Primary Industry and Regional Development, 3 Baron-Hay Court, South Perth, WA, 6151, Australia.
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, 434025, Hubei, China.
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30
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Fang Y, Zhang X, Zhang X, Tong T, Zhang Z, Wu G, Hou L, Zheng J, Niu C, Li J, Wang W, Wang H, Xue D. A High-Density Genetic Linkage Map of SLAFs and QTL Analysis of Grain Size and Weight in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2020; 11:620922. [PMID: 33424912 PMCID: PMC7793689 DOI: 10.3389/fpls.2020.620922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 11/26/2020] [Indexed: 05/12/2023]
Abstract
Grain size is an important agronomic trait determines yield in barley, and a high-density genetic map is helpful to accurately detect quantitative trait loci (QTLs) related to grain traits. Using specific-locus amplified fragment sequencing (SLAF-seq) technology, a high-density genetic map was constructed with a population of 134 recombinant inbred lines (RILs) deriving from a cross between Golden Promise (GP) and H602, which contained 12,635 SLAFs with 26,693 SNPs, and spanned 896.74 cM with an average interval of 0.07 cM on seven chromosomes. Based on the map, a total of 16 QTLs for grain length (GL), grain width and thousand-grain weight were detected on 1H, 2H, 4H, 5H, and 6H. Among them, a major QTL locus qGL1, accounting for the max phenotypic variance of 16.7% was located on 1H, which is a new unreported QTL affecting GL. In addition, the other two QTLs, qGL5 and qTGW5, accounting for the max phenotypic variances of 20.7 and 21.1%, respectively, were identified in the same region, and sequencing results showed they are identical to HvDep1 gene. These results indicate that it is a feasible approach to construct a high-quality genetic map for QTL mapping by using SLAF markers, and the detected major QTLs qGL1, qGL5, and qTGW5 are useful for marker-assisted selection (MAS) of grain size in barley breeding.
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Affiliation(s)
- Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaoqin Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Tao Tong
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ziling Zhang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Gengwei Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Junjun Zheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Chunyu Niu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Jia Li
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Wenjia Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hua Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- *Correspondence: Hua Wang,
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Dawei Xue,
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31
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Bustos‐Korts D, Dawson IK, Russell J, Tondelli A, Guerra D, Ferrandi C, Strozzi F, Nicolazzi EL, Molnar‐Lang M, Ozkan H, Megyeri M, Miko P, Çakır E, Yakışır E, Trabanco N, Delbono S, Kyriakidis S, Booth A, Cammarano D, Mascher M, Werner P, Cattivelli L, Rossini L, Stein N, Kilian B, Waugh R, van Eeuwijk FA. Exome sequences and multi-environment field trials elucidate the genetic basis of adaptation in barley. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 99:1172-1191. [PMID: 31108005 PMCID: PMC6851764 DOI: 10.1111/tpj.14414] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/30/2019] [Accepted: 05/13/2019] [Indexed: 05/25/2023]
Abstract
Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.
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Affiliation(s)
- Daniela Bustos‐Korts
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
| | - Ian K. Dawson
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Joanne Russell
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Alessandro Tondelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Davide Guerra
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Chiara Ferrandi
- PTP Science ParkVia Einstein, Loc. Cascina Codazza26900LodiItaly
| | | | | | - Marta Molnar‐Lang
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Hakan Ozkan
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Maria Megyeri
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Peter Miko
- Agricultural InstituteCentre for Agricultural ResearchHungarian Academy of Sciences2462MartonvásárHungary
| | - Esra Çakır
- University of ÇukurovaFaculty of AgricultureDepartment of Field Crops01330AdanaTurkey
| | - Enes Yakışır
- Bahri Dagdas International Agricultural Research InstituteKonyaTurkey
| | - Noemi Trabanco
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Stefano Delbono
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | | | - Allan Booth
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Davide Cammarano
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Peter Werner
- KWS UK Ltd56 Church StreetThriplow, RoystonSG8 7REUK
| | - Luigi Cattivelli
- CREA – Research Centre for Genomics and BioinformaticsVia S. Protaso 30229017Fiorenzuola d'ArdaItaly
| | - Laura Rossini
- Università degli Studi di Milano – DiSAAVia Celoria 220133MilanoItaly
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)06466SeelandGermany
- Present address:
Global Crop Diversity TrustPlatz der Vereinten Nationen 753113BonnGermany
| | - Robbie Waugh
- Cell and Molecular SciencesJames Hutton InstituteInvergowrie, DundeeUK
- Division of Plant SciencesSchool of Life SciencesUniversity of DundeeDow StreetDundeeDD1 5EHUK
| | - Fred A. van Eeuwijk
- BiometrisWageningen University and Research CentrePO Box 166700 ACWageningenThe Netherlands
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Schreiber M, Barakate A, Uzrek N, Macaulay M, Sourdille A, Morris J, Hedley PE, Ramsay L, Waugh R. A highly mutagenised barley ( cv. Golden Promise) TILLING population coupled with strategies for screening-by-sequencing. PLANT METHODS 2019; 15:99. [PMID: 31462905 PMCID: PMC6708184 DOI: 10.1186/s13007-019-0486-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/16/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND We developed and characterised a highly mutagenised TILLING population of the barley (Hordeum vulgare) cultivar Golden Promise. Golden Promise is the 'reference' genotype for barley transformation and a primary objective of using this cultivar was to be able to genetically complement observed mutations directly in order to prove gene function. Importantly, a reference genome assembly of Golden Promise has also recently been developed. As our primary interest was to identify mutations in genes involved in meiosis and recombination, to characterise the population we focused on a set of 46 genes from the literature that are possible meiosis gene candidates. RESULTS Sequencing 20 plants from the population using whole exome capture revealed that the mutation density in this population is high (one mutation every 154 kb), and consequently even in this small number of plants we identified several interesting mutations. We also recorded some issues with seed availability and germination. We subsequently designed and applied a simple two-dimensional pooling strategy to identify mutations in varying numbers of specific target genes by Illumina short read pooled-amplicon sequencing and subsequent deconvolution. In parallel we assembled a collection of semi-sterile mutants from the population and used a custom exome capture array targeting the 46 candidate meiotic genes to identify potentially causal mutations. CONCLUSIONS We developed a highly mutagenised barley TILLING population in the transformation competent cultivar Golden Promise. We used novel and cost-efficient screening approaches to successfully identify a broad range of potentially deleterious variants that were subsequently validated by Sanger sequencing. These resources combined with a high-quality genome reference sequence opens new possibilities for efficient functional gene validation.
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Affiliation(s)
- Miriam Schreiber
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Abdellah Barakate
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Nicola Uzrek
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Adeline Sourdille
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Jenny Morris
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Pete E. Hedley
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA Scotland UK
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee, DD2 5DA Scotland UK
- School of Agriculture and Wine, University of Adelaide, Plant Genome Building, Waite Campus, Urrbrae, Adelaide, SA Australia
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33
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Larson S, DeHaan L, Poland J, Zhang X, Dorn K, Kantarski T, Anderson J, Schmutz J, Grimwood J, Jenkins J, Shu S, Crain J, Robbins M, Jensen K. Genome mapping of quantitative trait loci (QTL) controlling domestication traits of intermediate wheatgrass (Thinopyrum intermedium). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2325-2351. [PMID: 31172227 DOI: 10.1007/s00122-019-03357-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 05/02/2019] [Indexed: 05/14/2023]
Abstract
Allohexaploid (2n = 6x = 42) intermediate wheatgrass (Thinopyrum intermedium), abbreviated IWG, is an outcrossing perennial grass belonging to the tertiary gene pool of wheat. Perenniality would be valuable option for grain production, but attempts to introgress this complex trait from wheat-Thinopyrum hybrids have not been commercially successful. Efforts to breed IWG itself as a dual-purpose forage and grain crop have demonstrated useful progress and applications, but grain yields are significantly less than wheat. Therefore, genetic and physical maps have been developed to accelerate domestication of IWG. Herein, these maps were used to identify quantitative trait loci (QTLs) and candidate genes associated with IWG grain production traits in a family of 266 full-sib progenies derived from two heterozygous parents, M26 and M35. Transgressive segregation was observed for 17 traits related to seed size, shattering, threshing, inflorescence capacity, fertility, stem size, and flowering time. A total of 111 QTLs were detected in 36 different regions using 3826 genotype-by-sequence markers in 21 linkage groups. The most prominent QTL had a LOD score of 15 with synergistic effects of 29% and 22% over the family means for seed retention and percentage of naked seeds, respectively. Many QTLs aligned with one or more IWG gene models corresponding to 42 possible domestication orthogenes including the wheat Q and RHT genes. A cluster of seed-size and fertility QTLs showed possible alignment to a putative Z self-incompatibility gene, which could have detrimental grain-yield effects when genetic variability is low. These findings elucidate pathways and possible hurdles in the domestication of IWG.
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Affiliation(s)
- Steve Larson
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA.
| | - Lee DeHaan
- The Land Institute, 2440 E. Water Well Rd, Salina, KS, 67401, USA
| | - Jesse Poland
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Xiaofei Zhang
- Department of Horticultural Science, North Carolina State University, 212 Kilgore Hall, 2721 Founders Drive, PO Box 7609, Raleigh, NC, 27607, USA
| | - Kevin Dorn
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Traci Kantarski
- American Association for the Advancement of Science, Science and Technology Policy Fellow at the United States Department of Agriculture, Animal and Plant Health Inspection Service, 4700 River Road, Riverdale, MD, 20737, USA
| | - James Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Buford Circle, St. Paul, MN, 55108, USA
| | - Jeremy Schmutz
- Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jane Grimwood
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Jerry Jenkins
- Hudson Alpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | - Shengqiang Shu
- Department of Energy, Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jared Crain
- Department of Plant Pathology, Kansas State University, 4024 Throckmorton, Manhattan, KS, 66506, USA
| | - Matthew Robbins
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
| | - Kevin Jensen
- United States Department of Agriculture, Agriculture Research Service, Forage and Range Research, Utah State University, Logan, UT, 84322, USA
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34
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Vavilova VY, Konopatskaia ID, Blinov AG, Goncharov NP. Interspecific Polymorphism of DEP1 Genes and the Spike Shape in Wheats. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419070147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Xu R, Li N, Li Y. Control of grain size by G protein signaling in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:533-540. [PMID: 30597738 DOI: 10.1111/jipb.12769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/24/2018] [Indexed: 06/09/2023]
Abstract
Heterotrimeric G proteins are involved in multiple cellular processes in eukaryotes by sensing and transducing various signals. G protein signaling in plants is quite different from that in animals, and the mechanisms of plant G protein signaling are still largely unknown. Several recent studies have provided new insights into the mechanisms of G protein signaling in rice grain size and yield control. In this review, we summarize recent advances on the function of G proteins in rice grain size control and discuss the potential genetic and molecular mechanisms of plant G protein signaling.
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Affiliation(s)
- Ran Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
| | - Na Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Center for Excellence in Molecular Plant Sciences, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
- The University of Chinese Academy of Sciences, Beijing 100039, China
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36
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Pandey S. Heterotrimeric G-Protein Signaling in Plants: Conserved and Novel Mechanisms. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:213-238. [PMID: 31035831 DOI: 10.1146/annurev-arplant-050718-100231] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Heterotrimeric GTP-binding proteins are key regulators of a multitude of signaling pathways in all eukaryotes. Although the core G-protein components and their basic biochemistries are broadly conserved throughout evolution, the regulatory mechanisms of G proteins seem to have been rewired in plants to meet specific needs. These proteins are currently the focus of intense research in plants due to their involvement in many agronomically important traits, such as seed yield, organ size regulation, biotic and abiotic stress responses, symbiosis, and nitrogen use efficiency. The availability of massive sequence information from a variety of plant species, extensive biochemical data generated over decades, and impressive genetic resources for plant G proteins have made it possible to examine their role, unique properties, and novel regulation. This review focuses on some recent advances in our understanding of the mechanistic details of this critical signaling pathway to enable the precise manipulation and generation of plants to meet future needs.
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Affiliation(s)
- Sona Pandey
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
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37
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Wang Q, Sun G, Ren X, Du B, Cheng Y, Wang Y, Li C, Sun D. Dissecting the Genetic Basis of Grain Size and Weight in Barley ( Hordeum vulgare L.) by QTL and Comparative Genetic Analyses. FRONTIERS IN PLANT SCIENCE 2019; 10:469. [PMID: 31105718 PMCID: PMC6491919 DOI: 10.3389/fpls.2019.00469] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/28/2019] [Indexed: 05/23/2023]
Abstract
Grain size and weight are crucial components of barley yield and quality and are the target characteristics of domestication and modern breeding. Despite this, little is known about the genetic and molecular mechanisms of grain size and weight in barley. Here, we evaluated nine traits determining grain size and weight, including thousand grain weight (Tgw), grain length (Gl), grain width (Gw), grain length-width ratio (Lwr), grain area (Ga), grain perimeter (Gp), grain diameter (Gd), grain roundness (Gr), and factor form density (Ffd), in a double haploid (DH) population for three consecutive years. Using five mapping methods, we successfully identified 60 reliable QTLs and 27 hotspot regions that distributed on all chromosomes except 6H which controls the nine traits of grain size and weight. Moreover, we also identified 164 barley orthologs of 112 grain size/weight genes from rice, maize, wheat and 38 barley genes that affect grain yield. A total of 45 barley genes or orthologs were identified as potential candidate genes for barley grain size and weight, including 12, 20, 9, and 4 genes or orthologs for barley, rice, maize, and wheat, respectively. Importantly, 20 of them were located in the 14 QTL hotspot regions on chromosome 1H, 2H, 3H, 5H, and 7H, which controls barley grain size and weight. These results indicated that grain size/weight genes of other cereal species might have the same or similar functions in barley. Our findings provide new insights into the understanding of the genetic basis of grain size and weight in barley, and new information to facilitate high-yield breeding in barley. The function of these potential candidate genes identified in this study are worth exploring and studying in detail.
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Affiliation(s)
- Qifei Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Genlou Sun
- Department of Biology, Saint Mary’s University, Halifax, NS, Canada
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Binbin Du
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yun Cheng
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yixiang Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Dongfa Sun
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, China
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38
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Watt C, Zhou G, McFawn LA, Chalmers KJ, Li C. Fine mapping of qGL5H, a major grain length locus in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:883-893. [PMID: 30465063 DOI: 10.1007/s00122-018-3243-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 11/16/2018] [Indexed: 05/05/2023]
Abstract
A major grain length QTL on chromosome 5H was fine mapped from 180.5 to 1.7 Mb. Quantitative trait loci (QTLs) mapping has been used extensively in barley to detect QTLs that underlie complex traits such as grain size. In the present study, we utilised 312 double haploid lines derived from a cross between two Australian malting varieties, Vlamingh and Buloke, to dissect the genetic control of a number of grain size characteristics. Digital image analysis was used to measure grain size characteristics including length, width, thickness and plumpness which are important traits influencing barley yield and grain physical quality. Using data from four independent environments and molecular marker genotype data, we identified 23 significant QTLs for these four traits, ten of which were consensus QTLs and identified in two or more environments. A QTL region on chromosome 5H designated qGL5H that was associated with grain size was fine mapped to a 1.7 Mb interval. qGL5H was able to explain 21.6% of phenotypic variation for grain length within the population. This major QTL is an appropriate candidate for further genetic dissection.
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Affiliation(s)
- Calum Watt
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Gaofeng Zhou
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia
| | - Lee-Anne McFawn
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia
| | | | - Chengdao Li
- Western Barley Genetic Alliance, Murdoch University, Perth, WA, Australia.
- Western Australian State Agricultural Biotechnology Centre, Murdoch University, Perth, WA, Australia.
- Department of Primary Industry and Regional Development, Perth, WA, Australia.
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39
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Dong H, Yan S, Liu J, Liu P, Sun J. TaCOLD1 defines a new regulator of plant height in bread wheat. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:687-699. [PMID: 30183124 PMCID: PMC6381784 DOI: 10.1111/pbi.13008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 08/14/2018] [Accepted: 08/23/2018] [Indexed: 05/21/2023]
Abstract
Plant height is among the most important agronomic traits that influence crop yield. However, in addition to the Rht-1 alleles, the molecular basis of plant height in bread wheat remains largely unclear. Based on wheat gene expression profiling analysis, we identify a light-regulated gene from bread wheat, designated as TaCOLD1, whose encoding protein is homologous to cold sensor COLD1 in rice. We show that TaCOLD1 protein is localized to the endoplasmic reticulum (ER) and plasma membrane. Phenotypic analyses show that overexpression of a mutated form of TaCOLD1 (M187K) in bread wheat cultivar Kenong199 (Rht-B1b) background resulted in an obvious reduction in plant height. Further, we demonstrate that the hydrophilic loop of TaCOLD1 (residues 178-296) can interact with TaGα-7A (the α subunit of heterotrimeric G protein) protein but not TaGα-1B, and the mutation (M187K) in TaCOLD1 remarkably enhances its interaction with TaGα-7A. Physical interaction analyses show that the C-terminal region of TaGα-7A, which is lacking in the TaGα-1B protein, is necessary for its interaction with TaCOLD1. Intriguingly, the C-terminal region of TaGα-7A is also physically associated with the TaDEP1 protein (an atypical Gγ subunit). Significantly, we discover that TaCOLD1 and mTaCOLD1 (M187K) can interfere with the physical association between TaGα-7A and TaDEP1. Together, this study reveals that TaCOLD1 acts as a novel regulator of plant height through interfering with the formation of heterotrimeric G protein complex in bread wheat and is a valuable target for the engineering of wheat plant architecture.
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Affiliation(s)
- Huixue Dong
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Suli Yan
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jie Liu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Pan Liu
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Jiaqiang Sun
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
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40
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Roy Choudhury S, Marlin MA, Pandey S. The Role of Gβ Protein in Controlling Cell Expansion via Potential Interaction with Lipid Metabolic Pathways. PLANT PHYSIOLOGY 2019; 179:1159-1175. [PMID: 30622152 PMCID: PMC6393804 DOI: 10.1104/pp.18.01312] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 12/10/2018] [Indexed: 05/23/2023]
Abstract
Heterotrimeric G-proteins influence almost all aspects of plant growth, development, and responses to biotic and abiotic stresses in plants, likely via their interaction with specific effectors. However, the identity of such effectors and their mechanism of action are mostly unknown. While investigating the roles of different G-protein subunits in modulating the oil content in Camelina (Camelina sativa), an oil seed crop, we uncovered a role of Gβ proteins in controlling anisotropic cell expansion. Knockdown of Gβ genes causes reduced longitudinal and enhanced transverse expansion, resulting in altered cell, tissue, and organ shapes in transgenic plants during vegetative and reproductive development. These plants also exhibited substantial changes in their fatty acid and phospholipid profiles, which possibly leads to the increased oil content of the transgenic seeds. This increase is potentially caused by the direct interaction of Gβ proteins with a specific patatin-like phospholipase, pPLAIIIδ. Camelina plants with suppressed Gβ expression exhibit higher lipase activity, and show phenotypes similar to plants overexpressing pPLAIIIδ, suggesting that the Gβ proteins are negative regulators of pPLAIIIδ. These results reveal interactions between the G-protein-mediated and lipid signaling/metabolic pathways, where specific phospholipases may act as effectors that control key developmental and environmental responses of plants.
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Affiliation(s)
| | - Maria A Marlin
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
| | - Sona Pandey
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132
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Shaaf S, Bretani G, Biswas A, Fontana IM, Rossini L. Genetics of barley tiller and leaf development. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:226-256. [PMID: 30548413 DOI: 10.1111/jipb.12757] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/10/2018] [Indexed: 06/09/2023]
Abstract
In cereals, tillering and leaf development are key factors in the concept of crop ideotype, introduced in the 1960s to enhance crop yield, via manipulation of plant architecture. In the present review, we discuss advances in genetic analysis of barley shoot architecture, focusing on tillering, leaf size and angle. We also discuss novel phenotyping techniques, such as 2D and 3D imaging, that have been introduced in the era of phenomics, facilitating reliable trait measurement. We discuss the identification of genes and pathways that are involved in barley tillering and leaf development, highlighting key hormones involved in the control of plant architecture in barley and rice. Knowledge on genetic control of traits related to plant architecture provides useful resources for designing ideotypes for enhanced barley yield and performance.
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Affiliation(s)
- Salar Shaaf
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
| | | | - Abhisek Biswas
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
| | | | - Laura Rossini
- University of Milan, DiSAA, Via Celoria 2, 20133 Milan, Italy
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McKim SM. How plants grow up. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:257-277. [PMID: 30697935 DOI: 10.1111/jipb.12786] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/21/2019] [Indexed: 05/27/2023]
Abstract
A plant's lateral structures, such as leaves, branches and flowers, literally hinge on the shoot axis, making its integrity and growth fundamental to plant form. In all plants, subapical proliferation within the shoot tip displaces cells downward to extrude the cylindrical stem. Following the transition to flowering, many plants show extensive axial elongation associated with increased subapical proliferation and expansion. However, the cereal grasses also elongate their stems, called culms, due to activity within detached intercalary meristems which displaces cells upward, elevating the grain-bearing inflorescence. Variation in culm length within species is especially relevant to cereal crops, as demonstrated by the high-yielding semi-dwarfed cereals of the Green Revolution. Although previously understudied, recent renewed interest the regulation of subapical and intercalary growth suggests that control of cell division planes, boundary formation and temporal dynamics of differentiation, are likely critical mechanisms coordinating axial growth and development in plants.
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Affiliation(s)
- Sarah M McKim
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
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Bélanger S, Paquet-Marceau S, Díaz Lago JE, Belzile F. QTL mapping uncovers a semi-dwarf 1 (sdw1) allele in the barley (Hordeum vulgare) ND23049 line. Genome 2018; 61:429-436. [DOI: 10.1139/gen-2017-0211] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In barley, semi-dwarf varieties are attractive for their superior harvest index and lodging resistance, but many semi-dwarf barley genotypes suffer from poor spike emergence. We performed a genetic characterization of a semi-dwarf line (ND23049) that combines short stature, strong stiff culms, and adequate spike emergence. We developed a doubled haploid (DH) population derived by crossing ND23049 and the cultivar CLE253. A subset of 88 DH lines and parents were characterized for plant height in 2013 and 2014 and genotyped. In total, 1984 SNPs (345 unique loci) were used to produce a linkage map of 1127.1 cM. Three QTLs for plant height were detected in this population and coincided with the HvGA20ox2/Sdw1, HvBRI1/Uzu1, and HvPRR95 gene loci. The phenotypic variation explained by each QTL was 75.8%, 7.7%, and 4.1%, respectively, and jointly explained 83.3% (2013) and 87.7% (2014) of plant height. Our results suggest that ND23049 contributed the “short” allele at the HvGA20ox2/sdw1 locus while CLE253 provided “short” alleles at the HvBRI1/uzu1 and HvPRR95 loci. We identified a large deletion (at least 92.7 Kb), including HvGA20ox2 (Sdw1), as the causal mutation in ND23049. A set of tightly flanked SNP markers will help breeders to develop improved semi-dwarf varieties.
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Affiliation(s)
- Sébastien Bélanger
- Département de phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Stéphanie Paquet-Marceau
- Département de phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | | | - François Belzile
- Département de phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
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Pandey S, Vijayakumar A. Emerging themes in heterotrimeric G-protein signaling in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 270:292-300. [PMID: 29576082 DOI: 10.1016/j.plantsci.2018.03.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 01/18/2018] [Accepted: 03/01/2018] [Indexed: 05/28/2023]
Abstract
Heterotrimeric G-proteins are key signaling components involved during the regulation of a multitude of growth and developmental pathways in all eukaryotes. Although the core proteins (Gα, Gβ, Gγ subunits) and their basic biochemistries are conserved between plants and non-plant systems, seemingly different inherent properties of specific components, altered wirings of G-protein network architectures, and the presence of novel receptors and effector proteins make plant G-protein signaling mechanisms somewhat distinct from the well-established animal paradigm. G-protein research in plants is getting a lot of attention recently due to the emerging roles of these proteins in controlling many agronomically important traits. New findings on both canonical and novel G-protein components and their conserved and unique signaling mechanisms are expected to improve our understanding of this important module in affecting critical plant growth and development pathways and eventually their utilization to produce plants for the future needs. In this review, we briefly summarize what is currently known in plant G-protein research, describe new findings and how they are changing our perceptions of the field, and discuss important issues that still need to be addressed.
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Affiliation(s)
- Sona Pandey
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA.
| | - Anitha Vijayakumar
- Donald Danforth Plant Science Center, 975 N. Warson Road, St. Louis, MO, 63132, USA
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Kaur J, Roy Choudhury S, Vijayakumar A, Hovis L, Rhodes Z, Polzin R, Blumenthal D, Pandey S. Arabidopsis Type III Gγ Protein AGG3 Is a Positive Regulator of Yield and Stress Responses in the Model Monocot Setaria viridis. FRONTIERS IN PLANT SCIENCE 2018; 9:109. [PMID: 29479357 PMCID: PMC5811934 DOI: 10.3389/fpls.2018.00109] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/19/2018] [Indexed: 05/10/2023]
Abstract
Heterotrimeric G-proteins are key regulators of a multitude of growth and development pathways in eukaryotes. Along with the conserved G-protein components found in all organisms, plants have certain novel variants with unique architecture, which may be involved in the regulation of plant-specific traits. The higher plant-specific type III (or Class C) Gγ protein, which possesses a large C terminal extension, represented by AGG3 in Arabidopsis, is one such variant of canonical Gγ proteins. The type III Gγ proteins are involved in regulation of many agronomically important traits in plants, including seed yield, organ size regulation, abscisic acid (ABA)-dependent signaling and stress responses, and nitrogen use efficiency. However, the extant data, especially in the monocots, present a relatively complex and sometimes contradictory picture of the regulatory role of these proteins. It remains unclear if the positive traits observed in certain naturally occurring populations are due to the presence of specific allelic variants of the proteins or due to the altered expression of the gene itself. To address these possibilities, we have overexpressed the Arabidopsis AGG3 gene in the model monocot Setaria viridis and systematically evaluated its role in conferring agriculturally relevant phenotypes. Our data show that AtAGG3 is indeed functional in Setaria and suggest that a subset of the traits affected by the type III Gγ proteins are indeed positively correlated with the gene expression level, while others might have more complex, allele specific regulation.
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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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Braumann I, Dockter C, Beier S, Himmelbach A, Lok F, Lundqvist U, Skadhauge B, Stein N, Zakhrabekova S, Zhou R, Hansson M. Mutations in the gene of the Gα subunit of the heterotrimeric G protein are the cause for the brachytic1 semi-dwarf phenotype in barley and applicable for practical breeding. Hereditas 2017; 155:10. [PMID: 28878591 PMCID: PMC5583965 DOI: 10.1186/s41065-017-0045-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 08/21/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Short-culm mutants have been widely used in breeding programs to increase lodging resistance. In barley (Hordeum vulgare L.), several hundreds of short-culm mutants have been isolated over the years. The objective of the present study was to identify the Brachytic1 (Brh1) semi-dwarfing gene and to test its effect on yield and malting quality. RESULTS Double-haploid lines generated through a cross between a brh1.a mutant and the European elite malting cultivar Quench, showed good malting quality but a decrease in yield. Especially the activities of the starch degrading enzymes β-amylase and free limit dextrinase were high. A syntenic approach comparing markers in barley to those in rice (Oryza sativa L.), sorghum (Sorghum bicolor Moench) and brachypodium (Brachypodium distachyon P. Beauv) helped us to identify Brh1 as an orthologue of rice D1 encoding the Gα subunit of a heterotrimeric G protein. We demonstrated that Brh1 is allelic to Ari-m. Sixteen different mutant alleles were described at the DNA level. CONCLUSIONS Mutants in the Brh1 locus are deficient in the Gα subunit of a heterotrimeric G protein, which shows that heterotrimeric G proteins are important regulators of culm length in barley. Mutant alleles do not have any major negative effects on malting quality.
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Affiliation(s)
- Ilka Braumann
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Christoph Dockter
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Finn Lok
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Udda Lundqvist
- Nordic Genetic Resource Center (NordGen), Smedjevägen 3, SE-23053 Alnarp, Sweden
| | - Birgitte Skadhauge
- Carlsberg Research Laboratory, J. C. Jacobsens Gade 4, DK-1799 Copenhagen V, Denmark
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | | | - Ruonan Zhou
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, DE-06466 Stadt Seeland, Germany
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, SE-22362 Lund, Sweden
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Bayer MM, Rapazote-Flores P, Ganal M, Hedley PE, Macaulay M, Plieske J, Ramsay L, Russell J, Shaw PD, Thomas W, Waugh R. Development and Evaluation of a Barley 50k iSelect SNP Array. FRONTIERS IN PLANT SCIENCE 2017; 8:1792. [PMID: 29089957 PMCID: PMC5651081 DOI: 10.3389/fpls.2017.01792] [Citation(s) in RCA: 146] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 10/02/2017] [Indexed: 05/18/2023]
Abstract
High-throughput genotyping arrays continue to be an attractive, cost-effective alternative to sequencing based approaches. We have developed a new 50k Illumina Infinium iSelect genotyping array for barley, a cereal crop species of major international importance. The majority of SNPs on the array have been extracted from variants called in exome capture data of a wide range of European barley germplasm. We used the recently published barley pseudomolecule assembly to map the exome capture data, which allowed us to generate markers with accurate physical positions and detailed gene annotation. Markers from an existing and widely used barley 9k Infinium iSelect array were carried over onto the 50k chip for backward compatibility. The array design featured 49,267 SNP markers that converted into 44,040 working assays, of which 43,461 were scorable in GenomeStudio. Of the working assays, 6,251 are from the 9k iSelect platform. We validated the SNPs by comparing the genotype calls from the new array to legacy datasets. Rates of agreement averaged 98.1 and 93.9% respectively for the legacy 9k iSelect SNP set (Comadran et al., 2012) and the exome capture SNPs. To test the utility of the 50k chip for genetic mapping, we genotyped a segregating population derived from a Golden Promise × Morex cross (Liu et al., 2014) and mapped over 14,000 SNPs to genetic positions which showed a near exact correspondence to their known physical positions. Manual adjustment of the cluster files used by the interpreting software for genotype scoring improved results substantially, but migration of cluster files between sites led to a deterioration of results, suggesting that local adjustment of cluster files is required on a site-per-site basis. Information relating to the markers on the chip is available online at https://ics.hutton.ac.uk/50k.
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Affiliation(s)
- Micha M. Bayer
- The James Hutton Institute, Dundee, United Kingdom
- *Correspondence: Micha M. Bayer
| | | | | | | | | | | | - Luke Ramsay
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Paul D. Shaw
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Robbie Waugh
- The James Hutton Institute, Dundee, United Kingdom
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