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Kuczyńska A, Michałek M, Ogrodowicz P, Kempa M, Witaszak N, Dziurka M, Gruszka D, Daszkowska-Golec A, Szarejko I, Krajewski P, Mikołajczak K. Drought-induced molecular changes in crown of various barley phytohormone mutants. PLANT SIGNALING & BEHAVIOR 2024; 19:2371693. [PMID: 38923879 PMCID: PMC11210921 DOI: 10.1080/15592324.2024.2371693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
One of the main signal transduction pathways that modulate plant growth and stress responses, including drought, is the action of phytohormones. Recent advances in omics approaches have facilitated the exploration of plant genomes. However, the molecular mechanisms underlying the response in the crown of barley, which plays an essential role in plant performance under stress conditions and regeneration after stress treatment, remain largely unclear. The objective of the present study was the elucidation of drought-induced molecular reactions in the crowns of different barley phytohormone mutants. We verified the hypothesis that defects of gibberellins, brassinosteroids, and strigolactones action affect the transcriptomic, proteomic, and hormonal response of barley crown to the transitory drought influencing plant development under stress. Moreover, we assumed that due to the strong connection between strigolactones and branching the hvdwarf14.d mutant, with dysfunctional receptor of strigolactones, manifests the most abundant alternations in crowns and phenotype under drought. Finally, we expected to identify components underlying the core response to drought which are independent of the genetic background. Large-scale analyses were conducted using gibberellins-biosynthesis, brassinosteroids-signaling, and strigolactones-signaling mutants, as well as reference genotypes. Detailed phenotypic evaluation was also conducted. The obtained results clearly demonstrated that hormonal disorders caused by mutations in the HvGA20ox2, HvBRI1, and HvD14 genes affected the multifaceted reaction of crowns to drought, although the expression of these genes was not induced by stress. The study further detected not only genes and proteins that were involved in the drought response and reacted specifically in mutants compared to the reaction of reference genotypes and vice versa, but also the candidates that may underlie the genotype-universal stress response. Furthermore, candidate genes involved in phytohormonal interactions during the drought response were identified. We also found that the interplay between hormones, especially gibberellins and auxins, as well as strigolactones and cytokinins may be associated with the regulation of branching in crowns exposed to drought. Overall, the present study provides novel insights into the molecular drought-induced responses that occur in barley crowns.
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Affiliation(s)
- Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Martyna Michałek
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Kempa
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Natalia Witaszak
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Michał Dziurka
- Faculty of Natural Sciences, The Franciszek Górski Institute of Plant Physiology Polish Academy of Sciences, Krakow, Poland
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
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Ndreca B, Huttly A, Bibi S, Bayon C, Lund G, Ham J, Alarcón-Reverte R, Addy J, Tarkowská D, Pearce S, Hedden P, Thomas SG, Phillips AL. Stacked mutations in wheat homologues of rice SEMI-DWARF1 confer a novel semi-dwarf phenotype. BMC PLANT BIOLOGY 2024; 24:384. [PMID: 38724935 PMCID: PMC11080193 DOI: 10.1186/s12870-024-05098-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/03/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Semi-dwarfing alleles are used widely in cereals to confer improved lodging resistance and assimilate partitioning. The most widely deployed semi-dwarfing alleles in rice and barley encode the gibberellin (GA)-biosynthetic enzyme GA 20-OXIDASE2 (GA20OX2). The hexaploid wheat genome carries three homoeologous copies of GA20OX2, and because of functional redundancy, loss-of-function alleles of a single homoeologue would not be selected in wheat breeding programmes. Instead, approximately 70% of wheat cultivars carry gain-of-function mutations in REDUCED HEIGHT 1 (RHT1) genes that encode negative growth regulators and are degraded in response to GA. Semi-dwarf Rht-B1b or Rht-D1b alleles encode proteins that are insensitive to GA-mediated degradation. However, because RHT1 is expressed ubiquitously these alleles have pleiotropic effects that confer undesirable traits in some environments. RESULTS We have applied reverse genetics to combine loss-of-function alleles in all three homoeologues of wheat GA20OX2 and its paralogue GA20OX1 and evaluated their performance in three years of field trials. ga20ox1 mutants exhibited a mild height reduction (approximately 3%) suggesting GA20OX1 plays a minor role in stem elongation in wheat. ga20ox2 mutants have reduced GA1 content and are 12-32% shorter than their wild-type segregants, comparable to the effect of the Rht-D1b 'Green Revolution' allele. The ga20ox2 mutants showed no significant negative effects on yield components in the spring wheat variety 'Cadenza'. CONCLUSIONS Our study demonstrates that chemical mutagenesis can expand genetic variation in polyploid crops to uncover novel alleles despite the difficulty in identifying appropriate mutations for some target genes and the negative effects of background mutations. Field experiments demonstrate that mutations in GA20OX2 reduce height in wheat, but it will be necessary to evaluate the effect of these alleles in different genetic backgrounds and environments to determine their value in wheat breeding as alternative semi-dwarfing alleles.
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Affiliation(s)
- Barbora Ndreca
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Alison Huttly
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Sajida Bibi
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Nuclear Institute for Agriculture and Biology, Faisalabad, Punjab, Pakistan
| | - Carlos Bayon
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - George Lund
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Joshua Ham
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | | | - John Addy
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Danuše Tarkowská
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
| | - Stephen Pearce
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Peter Hedden
- Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
- Laboratory of Growth Regulators, Institute of Experimental Botany, Czech Academy of Sciences and Palacky University, Šlechtitelů 27, Olomouc, CZ 78371, Czech Republic
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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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Cheng J, Jia Y, Hill C, He T, Wang K, Guo G, Shabala S, Zhou M, Han Y, Li C. Diversity of Gibberellin 2-oxidase genes in the barley genome offers opportunities for genetic improvement. J Adv Res 2024:S2090-1232(23)00408-3. [PMID: 38199453 DOI: 10.1016/j.jare.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
INTRODUCTION Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the "Green Revolution", modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known. OBJECTIVES This study investigates the physiological function of two HvGA2ox genes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits. METHODS Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8a in barley and RNA-seq was conducted to compare the transcriptome between wild type and mutants. Also, field trials in multiple environments were performed to detect the functional haplotypes. RESULTS There were ten GA2oxs that distinctly expressed in shoot, tiller, inflorescence, grain, embryo and root. Knockdown of HvGA2ox9 did not affect plant height, while ga2ox8a mutants generated by CRISPR/Cas9 increased plant height and significantly altered seed width and weight due to the increased bioactive GA4 level. RNA-seq analysis revealed that genes involved in starch and sucrose metabolism were significantly decreased in the inflorescence of ga2ox8a mutants. Furthermore, haplotype analysis revealed one naturally occurring HvGA2ox8a haplotype was associated with decreased plant height, early flowering and wider and heavier seed. CONCLUSION Our results demonstrate the potential of manipulating GA2ox genes to fine tune GA signalling and biofunctions in desired plant tissues and open a promising avenue for minimising the trade-off effects of Green Revolution semi-dwarfing genes on grain size and weight. The knowledge will promote the development of next generation barley cultivars with better adaptation to a changing climate.
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Affiliation(s)
- Jingye Cheng
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia; Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yong Jia
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia
| | - Camilla Hill
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Tianhua He
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia
| | - Ke Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ganggang Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, TAS, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
| | - Chengdao Li
- Western Crop Genetics Alliance, Food Futures Institute, School of Agriculture, Murdoch University, WA, Australia; Agriculture and Food, Department of Primary Industries and Regional Development, South Perth, WA, Australia.
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Liaqat S, Ali Z, Saddique MAB, Ikram RM, Ali I. Comparative transcript abundance of gibberellin oxidases genes in two barley ( Hordeum vulgare) genotypes with contrasting lodging resistance under different regimes of water deficit. FUNCTIONAL PLANT BIOLOGY : FPB 2024; 51:FP23246. [PMID: 38252957 DOI: 10.1071/fp23246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024]
Abstract
Barley (Hordeum vulgare ) is the world's fourth most important cereal crop, and is particularly well adapted to harsh environments. However, lodging is a major productivity constraint causing 13-65% yield losses. Gibberellic acid (GA) homeostatic genes such as HvGA20ox, HvGA3ox and HvGA2ox are responsible for changes in plant phenotype for height and internodal length that contribute towards lodging resistance. This study explored the expression of different HvGAox transcripts in two contrasting barley genotypes (5-GSBON-18, lodging resistant; and 5-GSBON-70, lodging sensitive), which were sown both under controlled (hydroponic, completely randomised factorial design) and field conditions (split-plot, completely randomised block design) with two irrigation treatments (normal with three irrigation events; and water deficit with one irrigation event). In the hydroponic experiment, expression analysis was performed on seedlings at 0, ¾, 1½, 3 and 6h after application of treatment. In the field experiment, leaf, shoot nodes and internodes were sampled. Downregulation of HvGA20ox.1 transcript and 2-fold upregulation of HvGA2ox.2 transcript were observed in 5-GSBON-18 under water deficit conditions. This genotype also showed a significant reduction in plant height (18-20%), lodging (<10%), and increased grain yield (15-18%) under stress. Utilisation of these transcripts in barley breeding has the potential to reduce plant height, lodging and increased grain yield.
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Affiliation(s)
- Shoaib Liaqat
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan 60000, Pakistan
| | - Zulfiqar Ali
- Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan 60000, Pakistan; and Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad 38000, Pakistan; and Programs and Projects Department, Islamic Organization for Food Security, Astana, Kazakhstan
| | | | - Rao Muhammad Ikram
- Department of Agronomy, MNS University of Agriculture, Multan 60000, Pakistan
| | - Imtiaz Ali
- Regional Agricultural Research Institute, Bahawalpur 63100, Pakistan
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Manipulating GA-Related Genes for Cereal Crop Improvement. Int J Mol Sci 2022; 23:ijms232214046. [PMID: 36430524 PMCID: PMC9696284 DOI: 10.3390/ijms232214046] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/08/2022] [Accepted: 11/11/2022] [Indexed: 11/16/2022] Open
Abstract
The global population is projected to experience a rapid increase in the future, which poses a challenge to global food sustainability. The "Green Revolution" beginning in the 1960s allowed grain yield to reach two billion tons in 2000 due to the introduction of semi-dwarfing genes in cereal crops. Semi-dwarfing genes reduce the gibberellin (GA) signal, leading to short plant stature, which improves the lodging resistance and harvest index under modern fertilization practices. Here, we reviewed the literature on the function of GA in plant growth and development, and the role of GA-related genes in controlling key agronomic traits that contribute to grain yield in cereal crops. We showed that: (1) GA is a significant phytohormone in regulating plant development and reproduction; (2) GA metabolism and GA signalling pathways are two key components in GA-regulated plant growth; (3) GA interacts with other phytohormones manipulating plant development and reproduction; and (4) targeting GA signalling pathways is an effective genetic solution to improve agronomic traits in cereal crops. We suggest that the modification of GA-related genes and the identification of novel alleles without a negative impact on yield and adaptation are significant in cereal crop breeding for plant architecture improvement. We observed that an increasing number of GA-related genes and their mutants have been functionally validated, but only a limited number of GA-related genes have been genetically modified through conventional breeding tools and are widely used in crop breeding successfully. New genome editing technologies, such as the CRISPR/Cas9 system, hold the promise of validating the effectiveness of GA-related genes in crop development and opening a new venue for efficient and accelerated crop breeding.
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Ma Z, Jin YM, Wu T, Hu L, Zhang Y, Jiang W, Du X. OsDREB2B, an AP2/ERF transcription factor, negatively regulates plant height by conferring GA metabolism in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1007811. [PMID: 36388558 PMCID: PMC9650310 DOI: 10.3389/fpls.2022.1007811] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 10/05/2022] [Indexed: 05/31/2023]
Abstract
The AP2/ERF family is a large group of plant-specific transcription factors that play an important role in many biological processes, such as growth, development, and abiotic stress responses. OsDREB2B, a dehydration responsive factor (DRE/CRT) in the DREB subgroup of the AP2/ERF family, is associated with abiotic stress responses, such as cold, drought, salt, and heat stress, in Arabidopsis or rice. However, its role in regulating plant growth and development in rice is unclear. In this study, we reported a new function of OsDREB2B, which negatively regulates plant height in rice. Compared with wild type (WT), OsDREB2B-overexpressing (OE) rice exhibited dwarf phenotypes, such as reduction in plant height, internode length, and seed length, as well as grain yield, while the knockout mutants developed by CRISPR/Cas9 technology exhibited similar phenotypes. Spatial expression analysis revealed that OsDREB2B was highly expressed in the leaf sheaths. Under exogenous GA3 application, OsDREB2B expression was induced, and the length of the second leaf sheath of the OsDREB2B-OE lines recovered to that of the WT. OsDREB2B localized to the nucleus of the rice protoplast acted as a transcription activator and upregulated OsAP2-39 by directly binding to its promoter. OsDREB2B-OE lines reduced endogenous bioactive GA levels by downregulating seven GA biosynthesis genes and upregulating eight GA deactivation genes but not GA signaling genes. The yeast two-hybrid assay and bimolecular fluorescence complementation assay showed that OsDREB2B interacted with OsWRKY21. In summary, our study suggests that OsDREB2B plays a negative role in rice growth and development by regulating GA metabolic gene expression, which is mediated by OsAP2-39 and OsWRKY21, thereby reducing GA content and rice plant height.
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Affiliation(s)
- Ziming Ma
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Yong-Mei Jin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Tao Wu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lanjuan Hu
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Ying Zhang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Wenzhu Jiang
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Provincial Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
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Beyene G, Chauhan RD, Villmer J, Husic N, Wang N, Gebre E, Girma D, Chanyalew S, Assefa K, Tabor G, Gehan M, McGrone M, Yang M, Lenderts B, Schwartz C, Gao H, Gordon‐Kamm W, Taylor NJ, MacKenzie DJ. CRISPR/Cas9-mediated tetra-allelic mutation of the 'Green Revolution' SEMIDWARF-1 (SD-1) gene confers lodging resistance in tef (Eragrostis tef). PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1716-1729. [PMID: 35560779 PMCID: PMC9398311 DOI: 10.1111/pbi.13842] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/17/2023]
Abstract
Tef is a staple food and a valuable cash crop for millions of people in Ethiopia. Lodging is a major limitation to tef production, and for decades, the development of lodging resistant varieties proved difficult with conventional breeding approaches. We used CRISPR/Cas9 to introduce knockout mutations in the tef orthologue of the rice SEMIDWARF-1 (SD-1) gene to confer semidwarfism and ultimately lodging resistance. High frequency recovery of transgenic and SD-1 edited tef lines was achieved in two tef cultivars by Agrobacterium-mediated delivery into young leaf explants of gene editing reagents along with transformation and regeneration enhancing morphogenic genes, BABY BOOM (BBM) and WUSCHEL2 (WUS2). All of the 23 lines analyzed by next-generation sequencing had at least two or more alleles of SD-1 mutated. Of these, 83% had tetra-allelic frameshift mutations in the SD-1 gene in primary tef regenerants, which were inherited in subsequent generations. Phenotypic data generated on T1 and T2 generations revealed that the sd-1 lines have reduced culm and internode lengths with no reduction in either panicle or peduncle lengths. These characteristics are comparable with rice sd-1 plants. Measurements of lodging, in greenhouse-grown plants, showed that sd-1 lines have significantly higher resistance to lodging at the heading stage compared with the controls. This is the first demonstration of the feasibility of high frequency genetic transformation and CRISPR/Cas9-mediated genome editing in this highly valuable but neglected crop. The findings reported here highlight the potential of genome editing for the improvement of lodging resistance and other important traits in tef.
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Affiliation(s)
- Getu Beyene
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Nada Husic
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | | | | | - Dejene Girma
- Ethiopian Institute of Agricultural ResearchAddis AbabaEthiopia
| | | | - Kebebew Assefa
- Ethiopian Institute of Agricultural ResearchAddis AbabaEthiopia
| | | | - Malia Gehan
- Donald Danforth Plant Science CenterSt. LouisMOUSA
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Mikołajczak K, Kuczyńska A, Ogrodowicz P, Kiełbowicz-Matuk A, Ćwiek-Kupczyńska H, Daszkowska-Golec A, Szarejko I, Surma M, Krajewski P. High-throughput sequencing data revealed genotype-specific changes evoked by heat stress in crown tissue of barley sdw1 near-isogenic lines. BMC Genomics 2022; 23:177. [PMID: 35246029 PMCID: PMC8897901 DOI: 10.1186/s12864-022-08410-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND High temperature shock is becoming increasingly common in our climate, affecting plant growth and productivity. The ability of a plant to survive stress is a complex phenomenon. One of the essential tissues for plant performance under various environmental stimuli is the crown. However, the molecular characterization of this region remains poorly investigated. Gibberellins play a fundamental role in whole-plant stature formation. This study identified plant stature modifications and crown-specific transcriptome re-modeling in gibberellin-deficient barley sdw1.a (BW827) and sdw1.d (BW828) mutants exposed to increased temperature. RESULTS The deletion around the sdw1 gene in BW827 was found to encompass at least 13 genes with primarily regulatory functions. A bigger genetic polymorphism of BW828 than of BW827 in relation to wild type was revealed. Transcriptome-wide sequencing (RNA-seq) revealed several differentially expressed genes involved in gibberellin metabolism and heat response located outside of introgression regions. It was found that HvGA20ox4, a paralogue of the HvGA20ox2 gene, was upregulated in BW828 relative to other genotypes, which manifested as basal internode elongation. The transcriptome response to elevated temperature differed in the crown of sdw1.a and sdw1.d mutants; it was most contrasting for HvHsf genes upregulated under elevated temperature in BW828, whereas those specific to BW827 were downregulated. In-depth examination of sdw1 mutants revealed also some differences in their phenotypes and physiology. CONCLUSIONS We concluded that despite the studied sdw1 mutants being genetically related, their heat response seemed to be genotype-specific and observed differences resulted from genetic background diversity rather than single gene mutation, multiple gene deletion, or allele-specific expression of the HvGA20ox2 gene. Differences in the expressional reaction of genes to heat in different sdw1 mutants, found to be independent of the polymorphism, could be further explained by in-depth studies of the regulatory factors acting in the studied system. Our findings are particularly important in genetic research area since molecular response of crown tissue has been marginally investigated, and can be useful for wide genetic research of crops since barley has become a model plant for them.
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Affiliation(s)
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | | | | | - Agata Daszkowska-Golec
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Iwona Szarejko
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Maria Surma
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland.
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Phenotypic Characterization and Differential Gene Expression Analysis Reveal That Dwarf Mutant dwf Dwarfism Is Associated with Gibberellin in Eggplant. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae7050114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Dwarfism is a desirable trait in eggplant breeding, as it confers higher lodging resistance and allows simplified management and harvest. However, a few dwarf mutants have been reported, and the molecular mechanism underlying dwarfism in eggplant is completely unknown. Here, we report a dwarf mutant (dwf) isolated from an ethyl methyl sulfonate (EMS)-induced mutant library. The hypocotyl length, plant height, and length of internode cells of dwf were significantly decreased compared to those of the wild-type parent ‘14-345’ (WT). Differential gene expression analysis revealed that GA-related genes, including GA2ox and DELLA, were up-regulated whereas the gibberellin (GA3) content decreased in dwf. Moreover, exogenous GA3 treatment significantly increased the relative growth rate of dwf compared to WT, further indicating the important roles of GA in regulating the dwarf phenotype of dwf. Collectively, our findings shed light on GA-mediated dwarfism in dwf plants and offer a good germplasm that could be used for eggplant dwarfism breeding in the future.
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Vitale P, Fania F, Esposito S, Pecorella I, Pecchioni N, Palombieri S, Sestili F, Lafiandra D, Taranto F, De Vita P. QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents. Genes (Basel) 2021; 12:genes12040604. [PMID: 33923933 PMCID: PMC8074140 DOI: 10.3390/genes12040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023] Open
Abstract
Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.
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Affiliation(s)
- Paolo Vitale
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Fabio Fania
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, Italy
- Correspondence: (F.T.); (P.D.V.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
- Correspondence: (F.T.); (P.D.V.)
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Hill CB, Angessa TT, Zhang XQ, Chen K, Zhou G, Tan C, Wang P, Westcott S, Li C. A global barley panel revealing genomic signatures of breeding in modern Australian cultivars. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:419-434. [PMID: 33506596 DOI: 10.1111/tpj.15173] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 06/12/2023]
Abstract
The future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Today's gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact that breeding had on the genetic diversity of Hordeum vulgare (barley) released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined data set and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.
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Affiliation(s)
- Camilla Beate Hill
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Tefera Tolera Angessa
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Xiao-Qi Zhang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Kefei Chen
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
- Statistics for the Australian Grains Industry (SAGI) West, Faculty of Science and Engineering, Curtin University, Kent Street, Bentley, WA, 6102, Australia
| | - Gaofeng Zhou
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Cong Tan
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Penghao Wang
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | - Sharon Westcott
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, Agricultural Sciences, College of Science, Health, Engineering and Education, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
- Agriculture and Food, Department of Primary Industries and Regional Development, 3 Baron-Hay Ct, South Perth, WA, 6151, Australia
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Genomic Dissection of Peduncle Morphology in Barley through Nested Association Mapping. PLANTS 2020; 10:plants10010010. [PMID: 33374821 PMCID: PMC7823623 DOI: 10.3390/plants10010010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/18/2020] [Accepted: 12/20/2020] [Indexed: 11/24/2022]
Abstract
Straw biomass and stability are crucial for stable yields. Moreover, straw harbors the potential to serve as a valuable raw material for bio-economic processes. The peduncle is the top part of the last shoot internode and carries the spike. This study investigates the genetic control of barley peduncle morphology. Therefore, 1411 BC1S3 lines of the nested association mapping (NAM) population “Halle Exotic Barley 25” (HEB-25), generated by crossing the spring barley elite cultivar Barke with an assortment of 25 exotic barley accessions, were used. Applying 50k Illumina Infinium iSelect SNP genotyping yielded new insights and a better understanding of the quantitative trait loci (QTL) involved in controlling the peduncle diameter traits, we found the total thickness of peduncle tissues and the area of the peduncle cross-section. We identified three major QTL regions on chromosomes 2H and 3H mainly impacting the traits. Remarkably, the exotic allele at the QTL on chromosome 3H improved all three traits investigated in this work. Introgressing this QTL in elite cultivars might facilitate to adjust peduncle morphology for improved plant stability or enlarged straw biomass production independent of flowering time and without detrimental effects on grain yield.
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14
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Büttner B, Draba V, Pillen K, Schweizer G, Maurer A. Identification of QTLs conferring resistance to scald (Rhynchosporium commune) in the barley nested association mapping population HEB-25. BMC Genomics 2020; 21:837. [PMID: 33246416 PMCID: PMC7694317 DOI: 10.1186/s12864-020-07258-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 11/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in yield losses of up to 40%. To breed resistant cultivars the identification of quantitative trait loci (QTLs) conferring resistance to scald is necessary. Introgressing promising resistance alleles of wild barley is a way to broaden the genetic basis of scald resistance in cultivated barley. Here, we apply nested association mapping (NAM) to map resistance QTLs in the barley NAM population HEB-25, comprising 1420 lines in BC1S3 generation, derived from crosses of 25 wild barley accessions with cv. Barke. RESULTS In scald infection trials in the greenhouse variability of resistance across and within HEB-25 families was found. NAM based on 33,005 informative SNPs resulted in the identification of eight reliable QTLs for resistance against scald with most wild alleles increasing resistance as compared to cv. Barke. Three of them are located in the region of known resistance genes and two in the regions of QTLs, respectively. The most promising wild allele was found at Rrs17 in one specific wild donor. Also, novel QTLs with beneficial wild allele effects on scald resistance were detected. CONCLUSIONS To sum up, wild barley represents a rich resource for scald resistance. As the QTLs were linked to the physical map the identified candidate genes will facilitate cloning of the scald resistance genes. The closely linked flanking molecular markers can be used for marker-assisted selection of the respective resistance genes to integrate them in elite cultivars.
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Affiliation(s)
- Bianca Büttner
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Vera Draba
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany
| | - Günther Schweizer
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Halle, Germany.
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Ma Z, Wu T, Huang K, Jin YM, Li Z, Chen M, Yun S, Zhang H, Yang X, Chen H, Bai H, Du L, Ju S, Guo L, Bian M, Hu L, Du X, Jiang W. A Novel AP2/ERF Transcription Factor, OsRPH1, Negatively Regulates Plant Height in Rice. FRONTIERS IN PLANT SCIENCE 2020; 11:709. [PMID: 32528516 PMCID: PMC7266880 DOI: 10.3389/fpls.2020.00709] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/05/2020] [Indexed: 05/24/2023]
Abstract
The APETALA 2/ethylene response factors (AP2/ERF) are widespread in the plant kingdom and play essential roles in regulating plant growth and development as well as defense responses. In this study, a novel rice AP2/ERF transcription factor gene, OsRPH1, was isolated and functionally characterized. OsRPH1 falls into group-IVa of the AP2/ERF family. OsRPH1 protein was found to be localized in the nucleus and possessed transcriptional activity. Overexpression of OsRPH1 resulted in a decrease in plant height and length of internode and leaf sheath as well as other abnormal characters in rice. The length of the second leaf sheath of OsRPH1-overexpressing (OE) plants recovered to that of Kitaake (non-transgenic recipient) in response to exogenous gibberellin A3 (GA3) application. The expression of GA biosynthesis genes (OsGA20ox1-OsGA20ox4, OsGA3ox1, and OsGA3ox2) was significantly downregulated, whereas that of GA inactivation genes (OsGA2ox7, OsGA2ox9, and OsGA2ox10) was significantly upregulated in OsRPH1-OE plants. Endogenous bioactive GA contents significantly decreased in OsRPH1-OE plants. OsRPH1 interacted with a blue light receptor, OsCRY1b, in a blue light-dependent manner. Taken together, our results demonstrate that OsRPH1 negatively regulates plant height and bioactive GA content by controlling the expression of GA metabolism genes in rice. OsRPH1 is involved in blue light inhibition of leaf sheath elongation by interacting with OsCRY1b.
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Affiliation(s)
- Ziming Ma
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Tao Wu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Kai Huang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Yong-Mei Jin
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhao Li
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mojun Chen
- Jilin Academy of Agricultural Sciences, Changchun, China
| | - Sokyong Yun
- Kye Ung Sang College of Agriculture of Kim II Sung University, Pyongyang, North Korea
| | - Hongjia Zhang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xue Yang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Haoyuan Chen
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Huijiao Bai
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Shanshan Ju
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Liping Guo
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Mingdi Bian
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Lanjuan Hu
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Xinglin Du
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
| | - Wenzhu Jiang
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, Changchun, China
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Marone D, Rodriguez M, Saia S, Papa R, Rau D, Pecorella I, Laidò G, Pecchioni N, Lafferty J, Rapp M, Longin FH, De Vita P. Genome-Wide Association Mapping of Prostrate/Erect Growth Habit in Winter Durum Wheat. Int J Mol Sci 2020; 21:ijms21020394. [PMID: 31936286 PMCID: PMC7014441 DOI: 10.3390/ijms21020394] [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] [Received: 12/05/2019] [Revised: 12/28/2019] [Accepted: 01/06/2020] [Indexed: 02/08/2023] Open
Abstract
By selecting for prostrate growth habit of the juvenile phase of the cycle, durum wheat cultivars could be developed with improved competitive ability against weeds, and better soil coverage to reduce the soil water lost by evaporation. A panel of 184 durum wheat (Triticum turgidum subsp. durum) genotypes, previously genotyped with DArT-seq markers, was used to perform association mapping analysis of prostrate/erect growth habit trait and to identify candidate genes. Phenotypic data of plant growth habit were recorded during three consecutive growing seasons (2014–2016), two different growth conditions (field trial and greenhouse) and two sowing periods (autumn and spring). Genome-wide association study revealed significant marker-trait associations, twelve of which were specific for a single environment/year, 4 consistent in two environments, and two MTAs for the LSmeans were identified across all environments, on chromosomes 2B and 5A. The co-localization of some MTAs identified in this study with known vernalization and photoperiod genes demonstrated that the sensitivity to vernalization and photoperiod response are actually not only key components of spring/winter growth habit, but they play also an important role in defining the magnitude of the tiller angle during the tillering stage. Many zinc-finger transcription factors, such as C2H2 or CCCH-domain zinc finger proteins, known to be involved in plant growth habit and in leaf angle regulation were found as among the most likely candidate genes. The highest numbers of candidate genes putatively related to the trait were found on chromosomes 3A, 4B, 5A and 6A. Moreover, a bioinformatic approach has been considered to search for functional ortholog genes in wheat by using the sequence of rice and barley tiller angle-related genes. The information generated could be used to improve the understanding of the mechanisms that regulate the prostrate/erect growth habit in wheat and the adaptive potential of durum wheat under resource-limited environmental conditions.
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Affiliation(s)
- Daniela Marone
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
- Centro per la Conservazione e Valorizzazione della Biodiversità Vegetale, Università degli Studi di Sassari, SS 127bis, km 28.500 Surigheddu, 07041 Alghero, Italy
| | - Sergio Saia
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Research Centre for Cereal and Industrial Crops, CREA, SS 11, km 2.500, 13100 Vercelli, Italy
| | - Roberto Papa
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy;
| | - Domenico Rau
- Department of Agriculture, University of Sassari, Via E. de Nicola, 14, 07100 Sassari, Italy; (M.R.); (D.R.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Giovanni Laidò
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
| | - Julia Lafferty
- Saatzucht Donau GesmbH & CoKG, Saatzuchtstrasse 11, A-2301 Probstdorf, Austria;
| | - Matthias Rapp
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Friedrich H. Longin
- State Plant Breeding Institute, University of Hohenheim, Fruwirthstraße 21, 70593 Stuttgart, Germany; (M.R.); (F.H.L.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops, CREA, SS 673, km 25.200, 71122 Foggia, Italy; (D.M.); (S.S.); (I.P.); (G.L.); (N.P.)
- Correspondence: ; Tel.: +39-0881-714911
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Herzig P, Backhaus A, Seiffert U, von Wirén N, Pillen K, Maurer A. Genetic dissection of grain elements predicted by hyperspectral imaging associated with yield-related traits in a wild barley NAM population. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 285:151-164. [PMID: 31203880 DOI: 10.1016/j.plantsci.2019.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/08/2019] [Accepted: 05/10/2019] [Indexed: 05/05/2023]
Abstract
Enhancing the accumulation of essential mineral elements in cereal grains is of prime importance for combating human malnutrition. Biofortification by breeding holds great potential for improving nutrient accumulation in grains. However, conventional breeding approaches require element analysis of many grain samples, which causes high costs. Here we applied hyperspectral imaging to estimate the concentration of 15 grain elements (C, B, Ca, Cd, Cu, Fe, K, Mg, Mn, Mo, N, Na, P, S, Zn) in high-throughput in the wild barley nested association mapping (NAM) population HEB-25, comprising 1,420 BC1S3 lines derived from crossing 25 wild barley accessions with the cultivar 'Barke'. Nutrient concentrations varied largely with a multitude of lines having higher micronutrient concentration than 'Barke'. In a genome-wide association study (GWAS), we located 75 quantitative trait locus (QTL) hotspots, whereof many could be explained by major genes such as NO APICAL MERISTEM-1 (NAM-1) and PHOTOPERIOD 1 (Ppd-H1). The GWAS approach revealed exotic alleles that were able to increase grain element concentrations. Remarkably, a QTL linked to GIBBERELLIN 20 OXIDASE 2 (HvGA20ox2) significantly increased several grain elements without yield loss. We conclude that introgressing promising exotic alleles into elite breeding material can assist in improving the nutritional value of barley grains.
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Affiliation(s)
- Paul Herzig
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Backhaus
- Fraunhofer Institute for Factory Operation and Automation (IFF), Sandtorstraße 22, 39106 Magdeburg, Germany
| | - Udo Seiffert
- Fraunhofer Institute for Factory Operation and Automation (IFF), Sandtorstraße 22, 39106 Magdeburg, Germany
| | - Nicolaus von Wirén
- Molecular Plant Nutrition, Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Stadt Seeland, OT Gatersleben, Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Chair of Plant Breeding, Betty-Heimann-Str. 3, 06120 Halle, Germany.
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18
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Wiegmann M, Maurer A, Pham A, March TJ, Al-Abdallat A, Thomas WTB, Bull HJ, Shahid M, Eglinton J, Baum M, Flavell AJ, Tester M, Pillen K. Barley yield formation under abiotic stress depends on the interplay between flowering time genes and environmental cues. Sci Rep 2019; 9:6397. [PMID: 31024028 PMCID: PMC6484077 DOI: 10.1038/s41598-019-42673-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 04/05/2019] [Indexed: 01/28/2023] Open
Abstract
Since the dawn of agriculture, crop yield has always been impaired through abiotic stresses. In a field trial across five locations worldwide, we tested three abiotic stresses, nitrogen deficiency, drought and salinity, using HEB-YIELD, a selected subset of the wild barley nested association mapping population HEB-25. We show that barley flowering time genes Ppd-H1, Sdw1, Vrn-H1 and Vrn-H3 exert pleiotropic effects on plant development and grain yield. Under field conditions, these effects are strongly influenced by environmental cues like day length and temperature. For example, in Al-Karak, Jordan, the day length-sensitive wild barley allele of Ppd-H1 was associated with an increase of grain yield by up to 30% compared to the insensitive elite barley allele. The observed yield increase is accompanied by pleiotropic effects of Ppd-H1 resulting in shorter life cycle, extended grain filling period and increased grain size. Our study indicates that the adequate timing of plant development is crucial to maximize yield formation under harsh environmental conditions. We provide evidence that wild barley alleles, introgressed into elite barley cultivars, can be utilized to support grain yield formation. The presented knowledge may be transferred to related crop species like wheat and rice securing the rising global food demand for cereals.
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Affiliation(s)
- Mathias Wiegmann
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 3, 06120, Halle, Germany
| | - Andreas Maurer
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 3, 06120, Halle, Germany
| | - Anh Pham
- The University of Adelaide, School of Agriculture, Food and Wine, Adelaide, SA, 5064, Australia
| | - Timothy J March
- The University of Adelaide, School of Agriculture, Food and Wine, Adelaide, SA, 5064, Australia
- Rijk Zwaan Australia Pty. Ltd., PO Box 284, Daylesford, 3460, Australia
| | - Ayed Al-Abdallat
- The University of Jordan, Faculty of Agriculture, Department of Horticulture and Crop Science, Amman, Jordan
| | | | - Hazel J Bull
- The James Hutton Institute, Invergrowie, Dundee, DD2 5DA, Scotland, UK
- Syngenta UK Ltd, Market Stainton, Market Rasen, Lincolnshire, LN8 5LJ, UK
| | - Mohammed Shahid
- International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Jason Eglinton
- The University of Adelaide, School of Agriculture, Food and Wine, Adelaide, SA, 5064, Australia
- Sugar Research Australia, 71378 Bruce Highway, Gordonvale, Queensland, Australia
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Dalia Building 2nd Floor, Bashir El Kassar Street, Verdun, Beirut, Lebanon
| | - Andrew J Flavell
- University of Dundee at JHI, School of Life Sciences, Invergrowie, Dundee, DD2 5DA, Scotland, UK
| | - Mark Tester
- King Abdullah University of Science and Technology, Biological and Environmental Sciences and Engineering, Thuwal, 23955-6900, Saudi Arabia
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg, Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 3, 06120, Halle, Germany.
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19
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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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Ford BA, Foo E, Sharwood R, Karafiatova M, Vrána J, MacMillan C, Nichols DS, Steuernagel B, Uauy C, Doležel J, Chandler PM, Spielmeyer W. Rht18 Semidwarfism in Wheat Is Due to Increased GA 2-oxidaseA9 Expression and Reduced GA Content. PLANT PHYSIOLOGY 2018; 177:168-180. [PMID: 29545269 PMCID: PMC5933146 DOI: 10.1104/pp.18.00023] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 03/04/2018] [Indexed: 05/04/2023]
Abstract
Semidwarfing genes have improved crop yield by reducing height, improving lodging resistance, and allowing plants to allocate more assimilates to grain growth. In wheat (Triticum aestivum), the Rht18 semidwarfing gene was identified and deployed in durum wheat before it was transferred into bread wheat, where it was shown to have agronomic potential. Rht18, a dominant and gibberellin (GA) responsive mutant, is genetically and functionally distinct from the widely used GA-insensitive semidwarfing genes Rht-B1b and Rht-D1b In this study, the Rht18 gene was identified by mutagenizing the semidwarf durum cultivar Icaro (Rht18) and generating mutants with a range of tall phenotypes. Isolating and sequencing chromosome 6A of these "overgrowth" mutants showed that they contained independent mutations in the coding region of GA2oxA9GA2oxA9 is predicted to encode a GA 2-oxidase that metabolizes GA biosynthetic intermediates into inactive products, effectively reducing the amount of bioactive GA (GA1). Functional analysis of the GA2oxA9 protein demonstrated that GA2oxA9 converts the intermediate GA12 to the inactive metabolite GA110 Furthermore, Rht18 showed higher expression of GA2oxA9 and lower GA content compared with its tall parent. These data indicate that the increased expression of GA2oxA9 in Rht18 results in a reduction of both bioactive GA content and plant height. This study describes a height-reducing mechanism that can generate new genetic diversity for semidwarfism in wheat by combining increased expression with mutations of specific amino acid residues in GA2oxA9.
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Affiliation(s)
- Brett A Ford
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Eloise Foo
- The School of Natural Sciences, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Robert Sharwood
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Miroslava Karafiatova
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371 Olomouc, Czech Republic
| | | | - David S Nichols
- Central Science Laboratories, University of Tasmania, Hobart, Tasmania 7001, Australia
| | | | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, CZ-78371 Olomouc, Czech Republic
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21
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Herzig P, Maurer A, Draba V, Sharma R, Draicchio F, Bull H, Milne L, Thomas WTB, Flavell AJ, Pillen K. Contrasting genetic regulation of plant development in wild barley grown in two European environments revealed by nested association mapping. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:1517-1531. [PMID: 29361127 PMCID: PMC5888909 DOI: 10.1093/jxb/ery002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 12/19/2017] [Indexed: 05/22/2023]
Abstract
Barley is cultivated more widely than the other major world crops because it adapts well to environmental constraints, such as drought, heat, and day length. To better understand the genetic control of local adaptation in barley, we studied development in the nested association mapping population HEB-25, derived from crossing 25 wild barley accessions with the cultivar 'Barke'. HEB-25 was cultivated in replicated field trials in Dundee (Scotland) and Halle (Germany), differing in regard to day length, precipitation, and temperature. Applying a genome-wide association study, we located 60 and 66 quantitative trait locus (QTL) regions regulating eight plant development traits in Dundee and Halle, respectively. A number of QTLs could be explained by known major genes such as PHOTOPERIOD 1 (Ppd-H1) and FLOWERING LOCUS T (HvFT-1) that regulate plant development. In addition, we observed that developmental traits in HEB-25 were partly controlled via genotype × environment and genotype × donor interactions, defined as location-specific and family-specific QTL effects. Our findings indicate that QTL alleles are available in the wild barley gene pool that show contrasting effects on plant development, which may be deployed to improve adaptation of cultivated barley to future environmental changes.
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Affiliation(s)
- Paul Herzig
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Vera Draba
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
- Interdisciplinary Center of Crop Plant Research (IZN), Halle, Germany
| | - Rajiv Sharma
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, Scotland, UK
| | - Fulvia Draicchio
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, Scotland, UK
| | - Hazel Bull
- The James Hutton Institute (JHI), Invergowrie, Dundee, Scotland, UK
| | - Linda Milne
- The James Hutton Institute (JHI), Invergowrie, Dundee, Scotland, UK
| | | | - Andrew J Flavell
- Division of Plant Sciences, University of Dundee at JHI, Invergowrie, Dundee, Scotland, UK
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin Luther University Halle-Wittenberg, Halle, Germany
- Correspondence:
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22
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Teplyakova S, Lebedeva M, Ivanova N, Horeva V, Voytsutskaya N, Kovaleva O, Potokina E. Impact of the 7-bp deletion in HvGA20ox2 gene on agronomic important traits in barley (Hordeum vulgare L.). BMC PLANT BIOLOGY 2017; 17:181. [PMID: 29143605 PMCID: PMC5688404 DOI: 10.1186/s12870-017-1121-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
BACKGROUND Alike to Reduced height-1 (Rht-1) genes in wheat and the semi dwarfing (sd-1) gene in rice, the sdw1/denso locus involved in the metabolism of the GA, was designated as the 'Green Revolution' gene in barley. The recent molecular characterization of the candidate gene HvGA20ox2 for sdw1/denso locus allows to estimate the impact of the functional polymorphism of this gene on the variation of agronomically important traits in barley. RESULTS We investigated the effect of the 7-bp deletion in exon 1 of HvGA20ox2 gene (sdw1.d mutation) on the variation of yield-related and malting quality traits in the population of DHLs derived from cross of medium tall barley Morex and semi-dwarf barley Barke. Segregation of plant height, flowering time, thousand grain weight, grain protein content and grain starch was evaluated in two diverse environments separated from one another by 15° of latitude. The 7-bp deletion in HvGA20ox2 gene reduced plant height by approximately 13 cm and delayed flowering time by 3-5 days in the barley segregating DHLs population independently on environmental cue. On other hand, the sdw1.d mutation did not affect significantly either grain quality traits (protein and starch content) or thousand grain weight. CONCLUSIONS The beneficial effect of the sdw1.d allele could be associated in barley with lodging resistance and extended period of vegetative growth allowing to accumulate additional biomass that supports higher yield in certain environments. However, no direct effect of the sdw1.d mutation on thousand grain weight or grain quality traits in barley was detected.
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Affiliation(s)
- Serafima Teplyakova
- Saint Petersburg State University, Universitetskaya emb.7/9, St. Petersburg, 199034, Russia
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Marina Lebedeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia
| | - Nadezhda Ivanova
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Valentina Horeva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Nina Voytsutskaya
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Olga Kovaleva
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia
| | - Elena Potokina
- Saint Petersburg State University, Universitetskaya emb.7/9, St. Petersburg, 199034, Russia.
- N.I. Vavilov Institute of Plant Genetic Resources (VIR), Bolshaya Morskaya, 42-44, 190000, St. Petersburg, Russia.
- Saint Petersburg State Forest Technical University, Institutskiy per, 5, 194021, St. Petersburg, Russia.
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23
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Xu Y, Jia Q, Zhou G, Zhang XQ, Angessa T, Broughton S, Yan G, Zhang W, Li C. Characterization of the sdw1 semi-dwarf gene in barley. BMC PLANT BIOLOGY 2017; 17:11. [PMID: 28086794 PMCID: PMC5237212 DOI: 10.1186/s12870-016-0964-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 12/23/2016] [Indexed: 05/02/2023]
Abstract
BACKGROUND The dwarfing gene sdw1 has been widely used throughout the world to develop commercial barley varieties. There are at least four different alleles at the sdw1 locus. RESULTS Mutations in the gibberellin 20-oxidase gene (HvGA20ox2) resulted in multiple alleles at the sdw1 locus. The sdw1.d allele from Diamant is due to a 7-bp deletion in exon 1, while the sdw1.c allele from Abed Denso has 1-bp deletion and a 4-bp insertion in the 5' untranslated region. The sdw1.a allele from Jotun resulted from a total deletion of the HvGA20ox2 gene. The structural changes result in lower gene expression in sdw1.d and lack of expression in sdw1.a. There are three HvGA20ox genes in the barley genome. The partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1and HvGA20ox3. A diagnostic molecular marker was developed to differentiate between the wild-type, sdw1.d and sdw1.a alleles and another molecular marker for differentiation of sdw1.c and sdw1.a. The markers were further tested in 197 barley varieties, out of which 28 had the sdw1.d allele and two varieties the sdw1.a allele. To date, the sdw1.d and sdw1.a alleles have only been detected in the modern barley varieties and lines. CONCLUSIONS The results provided further proof that the gibberellin 20-oxidase gene (HvGA20ox2) is the functional gene of the barley sdw1 mutants. Different deletions resulted in different functional alleles for different breeding purposes. Truncated protein could maintain partial function. Partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1 and HvGA20ox3.
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Affiliation(s)
- Yanhao Xu
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, 434000, China
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA6150, Australia
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province /College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China
| | - Gaofeng Zhou
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA6150, Australia
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA6150, Australia
| | - Tefera Angessa
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA6150, Australia
| | - Sue Broughton
- Department of Agriculture and Food Government of Western Australia, South Perth, WA6150, Australia
| | - George Yan
- College of Horticultural and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, 434000, China.
| | - Chengdao Li
- Hubei Collaborative Innovation Center for Grain Industry/College of Agriculture, Yangtze University, Jingzhou, Hubei, 434000, China.
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA6150, Australia.
- Department of Agriculture and Food Government of Western Australia, South Perth, WA6150, Australia.
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24
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Jia Q, Tan C, Wang J, Zhang XQ, Zhu J, Luo H, Yang J, Westcott S, Broughton S, Moody D, Li C. Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics 2016; 17:911. [PMID: 27835941 PMCID: PMC5106812 DOI: 10.1186/s12864-016-3247-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/02/2016] [Indexed: 12/04/2022] Open
Abstract
Background Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. .,Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China.
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hao Luo
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Sharon Westcott
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - David Moody
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
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25
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Mikołajczak K, Kuczyńska A, Krajewski P, Sawikowska A, Surma M, Ogrodowicz P, Adamski T, Krystkowiak K, Górny AG, Kempa M, Szarejko I, Guzy-Wróbelska J, Gudyś K. Quantitative trait loci for plant height in Maresi × CamB barley population and their associations with yield-related traits under different water regimes. J Appl Genet 2016; 58:23-35. [PMID: 27447461 PMCID: PMC5243891 DOI: 10.1007/s13353-016-0358-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 11/27/2022]
Abstract
High-yielding capacity of the modern barley varieties is mostly dependent on the sources of semi-dwarfness associated with the sdw1/denso locus. The objective of the study was to identify quantitative trait loci (QTLs) associated with the plant height and yield potential of barley recombinant inbred lines (RILs) grown under various soil moisture regimes. The plant material was developed from a hybrid between the Maresi (European cv.) and CamB (Syrian cv.). A total of 103 QTLs affecting analysed traits were detected and 36 of them showed stable effects over environments. In total, ten QTLs were found to be significant only under water shortage conditions. Nine QTLs affecting the length of main stem were detected on 2H-6H chromosomes. In four of the detected QTLs, alleles contributed by Maresi had negative effects on that trait, the most significant being the QLSt-3H.1-1 in the 3H.1 linkage group. The close linkage between QTLs identified around the sdw1/denso locus, with positive alleles contributed by Maresi, indicates that the semi-dwarf cv. Maresi could serve as a donor of favourable traits resulting in grain yield improvement, also under water scarcity. Molecular analyses revealed that the Syrian cv. also contributed alleles which increased the yield potential. Available barley resources of genomic annotations were employed to the biological interpretation of detected QTLs. This approach revealed 26 over-represented Gene Ontology terms. In the projected support intervals of QGWSl-5H.3-2 and QLSt-5H.3 on the chromosome 5H, four genes annotated to 'response to stress' were found. It suggests that these QTL-regions may be involved in a response of plant to a wide range of environmental disturbances.
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Affiliation(s)
- Krzysztof Mikołajczak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Aneta Sawikowska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Maria Surma
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Tadeusz Adamski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Karolina Krystkowiak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Andrzej G Górny
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Kempa
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40-032, Katowice, Poland
| | - Justyna Guzy-Wróbelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40-032, Katowice, Poland
| | - Kornelia Gudyś
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40-032, Katowice, Poland
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26
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Mikołajczak K, Ogrodowicz P, Gudyś K, Krystkowiak K, Sawikowska A, Frohmberg W, Górny A, Kędziora A, Jankowiak J, Józefczyk D, Karg G, Andrusiak J, Krajewski P, Szarejko I, Surma M, Adamski T, Guzy-Wróbelska J, Kuczyńska A. Quantitative Trait Loci for Yield and Yield-Related Traits in Spring Barley Populations Derived from Crosses between European and Syrian Cultivars. PLoS One 2016; 11:e0155938. [PMID: 27227880 PMCID: PMC4881963 DOI: 10.1371/journal.pone.0155938] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 05/08/2016] [Indexed: 11/18/2022] Open
Abstract
In response to climatic changes, breeding programmes should be aimed at creating new cultivars with improved resistance to water scarcity. The objective of this study was to examine the yield potential of barley recombinant inbred lines (RILs) derived from three cross-combinations of European and Syrian spring cultivars, and to identify quantitative trait loci (QTLs) for yield-related traits in these populations. RILs were evaluated in field experiments over a period of three years (2011 to 2013) and genotyped with simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers; a genetic map for each population was constructed and then one consensus map was developed. Biological interpretation of identified QTLs was achieved by reference to Ensembl Plants barley gene space. Twelve regions in the genomes of studied RILs were distinguished after QTL analysis. Most of the QTLs were identified on the 2H chromosome, which was the hotspot region in all three populations. Syrian parental cultivars contributed alleles decreasing traits' values at majority of QTLs for grain weight, grain number, spike length and time to heading, and numerous alleles increasing stem length. The phenomic and molecular approaches distinguished the lines with an acceptable grain yield potential combining desirable features or alleles from their parents, that is, early heading from the Syrian breeding line (Cam/B1/CI08887//CI05761) and short plant stature from the European semidwarf cultivar (Maresi).
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Affiliation(s)
- Krzysztof Mikołajczak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Kornelia Gudyś
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
| | - Karolina Krystkowiak
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Aneta Sawikowska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Wojciech Frohmberg
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Andrzej Górny
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Andrzej Kędziora
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Janusz Jankowiak
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Damian Józefczyk
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Grzegorz Karg
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Joanna Andrusiak
- Institute for Agricultural and Forest Environment, Polish Academy of Sciences, Bukowska 19, 60–809 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
| | - Maria Surma
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Tadeusz Adamski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Justyna Guzy-Wróbelska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellońska 28, 40–032 Katowice, Poland
- * E-mail: (AK); (JGW)
| | - Anetta Kuczyńska
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
- * E-mail: (AK); (JGW)
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