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Kumar APK, Boualem A, Bhattacharya A, Parikh S, Desai N, Zambelli A, Leon A, Chatterjee M, Bendahmane A. SMART--Sunflower Mutant population And Reverse genetic Tool for crop improvement. BMC PLANT BIOLOGY 2013; 13:38. [PMID: 23496999 PMCID: PMC3606330 DOI: 10.1186/1471-2229-13-38] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Accepted: 02/13/2013] [Indexed: 05/20/2023]
Abstract
BACKGROUND Sunflower (Helianthus annuus L.) is an important oilseed crop grown widely in various areas of the world. Classical genetic studies have been extensively undertaken for the improvement of this particular oilseed crop. Pertaining to this endeavor, we developed a "chemically induced mutated genetic resource for detecting SNP by TILLING" in sunflower to create new traits. RESULTS To optimize the EMS mutagenesis, we first conducted a "kill curve" analysis with a range of EMS dose from 0.5% to 3%. Based on the observed germination rate, a 50% survival rate i.e. LD50, treatment with 0.6% EMS for 8 hours was chosen to generate 5,000 M2 populations, out of which, 4,763 M3 plants with fertile seed set. Phenotypic characterization of the 5,000 M2 mutagenised lines were undertaken to assess the mutagenesis quality and to identify traits of interest. In the M2 population, about 1.1% of the plants showed phenotypic variations. The sunflower TILLING platform was setup using Endo-1-nuclease as mismatch detection system coupled with an eight fold DNA pooling strategy. As proof-of-concept, we screened the M2 population for induced mutations in two genes related to fatty acid biosynthesis, FatA an acyl-ACP thioesterase and SAD the stearoyl-ACP desaturase and identified a total of 26 mutations. CONCLUSION Based on the TILLING of FatA and SAD genes, we calculated the overall mutation rate to one mutation every 480 kb, similar to other report for this crop so far. As sunflower is a plant model for seed oil biosynthesis, we anticipate that the developed genetic resource will be a useful tool to identify novel traits for sunflower crop improvement.
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Affiliation(s)
- Anish PK Kumar
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Adnane Boualem
- INRA, UMR1165 Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- UEVE, UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- CNRS, ERL8196 UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
| | | | - Seema Parikh
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Nirali Desai
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
| | - Andres Zambelli
- Biotechnology Research Centre, Nutrisun Business Unit- Advanta Semillas SAIC, Belcarce, Argentina
| | - Alberto Leon
- Biotechnology Research Centre, Nutrisun Business Unit- Advanta Semillas SAIC, Belcarce, Argentina
| | - Manash Chatterjee
- Bench Bio Pvt Ltd., c/o Jai Research Foundation, Vapi, Gujarat, 396195, India
- National University of Ireland Galway (NUIG), Galway, Ireland
| | - Abdelhafid Bendahmane
- INRA, UMR1165 Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- UEVE, UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
- CNRS, ERL8196 UMR Unité de Recherche en Génomique Végétale URGV, Evry, F-91057, France
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202
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Okabe Y, Ariizumi T, Ezura H. Updating the Micro-Tom TILLING platform. BREEDING SCIENCE 2013; 63:42-8. [PMID: 23641180 PMCID: PMC3621444 DOI: 10.1270/jsbbs.63.42] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/25/2012] [Indexed: 05/25/2023]
Abstract
The dwarf tomato variety Micro-Tom is regarded as a model system for functional genomics studies in tomato. Various tomato genomic tools in the genetic background of Micro-Tom have been established, such as mutant collections, genome information and a metabolomic database. Recent advances in tomato genome sequencing have brought about a significant need for reverse genetics tools that are accessible to the larger community, because a great number of gene sequences have become available from public databases. To meet the requests from the tomato research community, we have developed the Micro-Tom Targeting-Induced Local Lesions IN Genomes (TILLING) platform, which is comprised of more than 5000 EMS-mutagenized lines. The platform serves as a reverse genetics tool for efficiently identifying mutant alleles in parallel with the development of Micro-Tom mutant collections. The combination of Micro-Tom mutant libraries and the TILLING approach enables researchers to accelerate the isolation of desirable mutants for unraveling gene function or breeding. To upgrade the genomic tool of Micro-Tom, the development of a new mutagenized population is underway. In this paper, the current status of the Micro-Tom TILLING platform and its future prospects are described.
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Affiliation(s)
- Yoshihiro Okabe
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Hiroshi Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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203
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Owatworakit A, Townsend B, Louveau T, Jenner H, Rejzek M, Hughes RK, Saalbach G, Qi X, Bakht S, Roy AD, Mugford ST, Goss RJM, Field RA, Osbourn A. Glycosyltransferases from oat (Avena) implicated in the acylation of avenacins. J Biol Chem 2013; 288:3696-704. [PMID: 23258535 PMCID: PMC3567625 DOI: 10.1074/jbc.m112.426155] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Revised: 12/18/2012] [Indexed: 11/06/2022] Open
Abstract
Plants produce a huge array of specialized metabolites that have important functions in defense against biotic and abiotic stresses. Many of these compounds are glycosylated by family 1 glycosyltransferases (GTs). Oats (Avena spp.) make root-derived antimicrobial triterpenes (avenacins) that provide protection against soil-borne diseases. The ability to synthesize avenacins has evolved since the divergence of oats from other cereals and grasses. The major avenacin, A-1, is acylated with N-methylanthranilic acid. Previously, we have cloned and characterized three genes for avenacin synthesis (for the triterpene synthase SAD1, a triterpene-modifying cytochrome P450 SAD2, and the serine carboxypeptidase-like acyl transferase SAD7), which form part of a biosynthetic gene cluster. Here, we identify a fourth member of this gene cluster encoding a GT belonging to clade L of family 1 (UGT74H5), and show that this enzyme is an N-methylanthranilic acid O-glucosyltransferase implicated in the synthesis of avenacin A-1. Two other closely related family 1 GTs (UGT74H6 and UGT74H7) are also expressed in oat roots. One of these (UGT74H6) is able to glucosylate both N-methylanthranilic acid and benzoic acid, whereas the function of the other (UGT74H7) remains unknown. Our investigations indicate that UGT74H5 is likely to be key for the generation of the activated acyl donor used by SAD7 in the synthesis of the major avenacin, A-1, whereas UGT74H6 may contribute to the synthesis of other forms of avenacin that are acylated with benzoic acid.
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Affiliation(s)
| | - Belinda Townsend
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom, and
| | | | - Helen Jenner
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom, and
| | - Martin Rejzek
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Richard K. Hughes
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Gerhard Saalbach
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Xiaoquan Qi
- From the Department of Metabolic Biology and
| | | | - Abhijeet Deb Roy
- the School of Chemical Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | | | - Rebecca J. M. Goss
- the School of Chemical Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Robert A. Field
- Department of Biological Chemistry, The John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom
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204
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Schornack S, Moscou MJ, Ward ER, Horvath DM. Engineering plant disease resistance based on TAL effectors. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:383-406. [PMID: 23725472 DOI: 10.1146/annurev-phyto-082712-102255] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Transcription activator-like (TAL) effectors are encoded by plant-pathogenic bacteria and induce expression of plant host genes. TAL effectors bind DNA on the basis of a unique code that specifies binding of amino acid residues in repeat units to particular DNA bases in a one-to-one correspondence. This code can be used to predict binding sites of natural TAL effectors and to design novel synthetic DNA-binding domains for targeted genome manipulation. Natural mechanisms of resistance in plants against TAL effector-containing pathogens have given insights into new strategies for disease control.
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Affiliation(s)
- Sebastian Schornack
- Sainsbury Laboratory, University of Cambridge, Cambridge, CB2 1LR, United Kingdom
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205
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High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING. PLoS One 2012. [PMID: 23185237 PMCID: PMC3504036 DOI: 10.1371/journal.pone.0047284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used. Methodology/Principal Findings To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results. Conclusions/Significance These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.
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206
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Rawat N, Sehgal SK, Joshi A, Rothe N, Wilson DL, McGraw N, Vadlani PV, Li W, Gill BS. A diploid wheat TILLING resource for wheat functional genomics. BMC PLANT BIOLOGY 2012; 12:205. [PMID: 23134614 PMCID: PMC3541219 DOI: 10.1186/1471-2229-12-205] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 10/29/2012] [Indexed: 05/08/2023]
Abstract
BACKGROUND Triticum monococcum L., an A genome diploid einkorn wheat, was the first domesticated crop. As a diploid, it is attractive genetic model for the study of gene structure and function of wheat-specific traits. Diploid wheat is currently not amenable to reverse genetics approaches such as insertion mutagenesis and post-transcriptional gene silencing strategies. However, TILLING offers a powerful functional genetics approach for wheat gene analysis. RESULTS We developed a TILLING population of 1,532 M2 families using EMS as a mutagen. A total of 67 mutants were obtained for the four genes studied. Waxy gene mutation frequencies are known to be 1/17.6 - 34.4 kb DNA in polyploid wheat TILLING populations. The T. monococcum diploid wheat TILLING population had a mutation frequency of 1/90 kb for the same gene. Lignin biosynthesis pathway genes- COMT1, HCT2, and 4CL1 had mutation frequencies of 1/86 kb, 1/92 kb and 1/100 kb, respectively. The overall mutation frequency of the diploid wheat TILLING population was 1/92 kb. CONCLUSION The mutation frequency of a diploid wheat TILLING population was found to be higher than that reported for other diploid grasses. The rate, however, is lower than tetraploid and hexaploid wheat TILLING populations because of the higher tolerance of polyploids to mutations. Unlike polyploid wheat, most mutants in diploid wheat have a phenotype amenable to forward and reverse genetic analysis and establish diploid wheat as an attractive model to study gene function in wheat. We estimate that a TILLING population of 5, 520 will be needed to get a non-sense mutation for every wheat gene of interest with 95% probability.
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Affiliation(s)
- Nidhi Rawat
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish K Sehgal
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
| | - Anupama Joshi
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
| | - Nolan Rothe
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
| | - Duane L Wilson
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
| | - Nathan McGraw
- Bioprocessing and Renewable Energy Laboratory, Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Praveen V Vadlani
- Bioprocessing and Renewable Energy Laboratory, Department of Grain Science and Industry, Kansas State University, Manhattan, KS, 66506, USA
| | - Wanlong Li
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, 57007, USA
| | - Bikram S Gill
- Wheat Genetic and Genomic Resources Center, Throckmorton Hall, Kansas State University, Manhattan, KS, 66506, USA
- Faculty of Science, Genomics and Biotechnology Section, Department of Biological Sciences, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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207
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D'Erfurth I, Le Signor C, Aubert G, Sanchez M, Vernoud V, Darchy B, Lherminier J, Bourion V, Bouteiller N, Bendahmane A, Buitink J, Prosperi JM, Thompson R, Burstin J, Gallardo K. A role for an endosperm-localized subtilase in the control of seed size in legumes. THE NEW PHYTOLOGIST 2012; 196:738-751. [PMID: 22985172 DOI: 10.1111/j.1469-8137.2012.04296.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 07/25/2012] [Indexed: 05/08/2023]
Abstract
Here, we report a subtilase gene (SBT1.1) specifically expressed in the endosperm of Medicago truncatula and Pisum sativum seeds during development, which is located at a chromosomal position coinciding with a seed weight quantitative trait locus (QTL). Association studies between SBT1.1 polymorphisms and seed weights in ecotype collections provided further evidence for linkage disequilibrium between the SBT1.1 locus and a seed weight locus. To investigate the possible contribution of SBT1.1 to the control of seed weight, a search for TILLING (Targeting Induced Local Lesions in Genomes) mutants was performed. An inspection of seed phenotype revealed a decreased weight and area of the sbt1.1 mutant seeds, thus inferring a role of SBT1.1 in the control of seed size in the forage and grain legume species. Microscopic analyses of the embryo, representing the major part of the seed, revealed a reduced number of cells in the MtP330S mutant, but no significant variation in cell size. SBT1.1 is therefore most likely to be involved in the control of cotyledon cell number, rather than cell expansion, during seed development. This raises the hypothesis of a role of SBT1.1 in the regulation of seed size by providing molecules that can act as signals to control cell division within the embryo.
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Affiliation(s)
- I D'Erfurth
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - C Le Signor
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - G Aubert
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - M Sanchez
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Vernoud
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - B Darchy
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Lherminier
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - V Bourion
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - N Bouteiller
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - A Bendahmane
- INRA/CNRS (Centre National de la Recherche Scientifique), Unité de Recherche en Génomique Végétale, CP5708, 91057, Evry, France
| | - J Buitink
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, 49045, Angers, France
| | - J M Prosperi
- INRA, UMR1334 Amélioration Génétique et Adaptation des Plantes, 34060, Montpellier, France
| | - R Thompson
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - J Burstin
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
| | - K Gallardo
- INRA (Institut National de la Recherche Agronomique), UMR1347 Agroécologie, BP 86510, F-21000, Dijon, France
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208
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Kurowska M, Labocha-Pawłowska A, Gnizda D, Maluszynski M, Szarejko I. Molecular analysis of point mutations in a barley genome exposed to MNU and gamma rays. Mutat Res 2012; 738-739:52-70. [PMID: 23085094 DOI: 10.1016/j.mrfmmm.2012.08.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Revised: 07/27/2012] [Accepted: 08/24/2012] [Indexed: 12/24/2022]
Abstract
We present studies aimed at determining the types and frequencies of mutations induced in the barley genome after treatment with chemical (N-methyl-N-nitrosourea, MNU) and physical (gamma rays) mutagens. We created M(2) populations of a doubled haploid line and used them for the analysis of mutations in targeted DNA sequences and over an entire barley genome using TILLING (Targeting Induced Local Lesions in Genomes) and AFLP (Amplified Fragment Length Polymorphism) technique, respectively. Based on the TILLING analysis of the total DNA sequence of 4,537,117bp in the MNU population, the average mutation density was estimated as 1/504kb. Only one nucleotide change was found after an analysis of 3,207,444bp derived from the highest dose of gamma rays applied. MNU was clearly a more efficient mutagen than gamma rays in inducing point mutations in barley. The majority (63.6%) of the MNU-induced nucleotide changes were transitions, with a similar number of G>A and C>T substitutions. The similar share of G>A and C>T transitions indicates a lack of bias in the repair of O(6)-methylguanine lesions between DNA strands. There was, however, a strong specificity of the nucleotide surrounding the O(6)-meG at the -1 position. Purines formed 81% of nucleotides observed at the -1 site. Scanning the barley genome with AFLP markers revealed ca. a three times higher level of AFLP polymorphism in MNU-treated as compared to the gamma-irradiated population. In order to check whether AFLP markers can really scan the whole barley genome for mutagen-induced polymorphism, 114 different AFLP products, were cloned and sequenced. 94% of bands were heterogenic, with some bands containing up to 8 different amplicons. The polymorphic AFLP products were characterised in terms of their similarity to the records deposited in a GenBank database. The types of sequences present in the polymorphic bands reflected the organisation of the barley genome.
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Affiliation(s)
- Marzena Kurowska
- Department of Genetics, University of Silesia, Katowice, Poland.
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209
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Scientific opinion addressing the safety assessment of plants developed using Zinc Finger Nuclease 3 and other Site‐Directed Nucleases with similar function. EFSA J 2012. [DOI: 10.2903/j.efsa.2012.2943] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
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210
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Xu J, Li M, Chen L, Wu G, Li H. Rapid generation of rice mutants via the dominant negative suppression of the mismatch repair protein OsPMS1. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:975-86. [PMID: 22688271 DOI: 10.1007/s00122-012-1888-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2012] [Accepted: 04/27/2012] [Indexed: 05/12/2023]
Abstract
Mismatch repair (MMR) is a conservative pathway for maintaining the genome integrity of different organisms. Although suppression of MMR has resulted in various mutation phenotypes in Arabidopsis, the use of this strategy for mutation breeding in major crops has not been reported. Here, we overexpressed a truncated version of the OsPMS1 protein in rice; this approach is expected to suppress the rice MMR system through a dominant negative mechanism. We observed a wide spectrum of mutation phenotypes in the progeny of the transgenic plants during seed germination and the plant growth stages. Genomic variations were detected with inter-simple sequence repeat (ISSR), and sequencing of the differential ISSR bands revealed that the mutation occurred as a point mutation or as microsatellite instability at high frequencies. Plant lines with agronomically important traits, such as salt and drought tolerance, various tiller number, and early flowering, were obtained. Furthermore, we obtained mutants with important traits that are free of the transgene. Together, these results demonstrate that MMR suppression can be used as an efficient strategy for mutation breeding in rice.
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Affiliation(s)
- Jie Xu
- Guangdong Provincial Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, People's Republic of China
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211
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High-throughput phenotyping of plant populations using a personal digital assistant. Methods Mol Biol 2012; 918:97-116. [PMID: 22893288 DOI: 10.1007/978-1-61779-995-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/27/2023]
Abstract
During many biological experiments voluminous data is acquired, which can be best collected with -portable data acquisition devices and later analyzed with a personal computer (PC). Public domain software catering to data acquisition and analysis is currently limited. The necessity of phenotyping large plant populations led to the development of the application "PHENOME" to manage the data. PHENOME allows acquisition of phenotypic data using a personal digital assistant (PDA) with a built-in barcode scanner. The acquired data can be exported to a customized database on a PC for further analysis and cataloging. PHENOME can be used for a variety of applications, for example high-throughput phenotyping of a mutagenized or mapping population, or phenotyping of several individuals in one or more ecological niches.
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212
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Xia Z, Watanabe S, Yamada T, Tsubokura Y, Nakashima H, Zhai H, Anai T, Sato S, Yamazaki T, Lü S, Wu H, Tabata S, Harada K. Positional cloning and characterization reveal the molecular basis for soybean maturity locus E1 that regulates photoperiodic flowering. Proc Natl Acad Sci U S A 2012; 109:E2155-64. [PMID: 22619331 PMCID: PMC3420212 DOI: 10.1073/pnas.1117982109] [Citation(s) in RCA: 256] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The complex and coordinated regulation of flowering has high ecological and agricultural significance. The maturity locus E1 has a large impact on flowering time in soybean, but the molecular basis for the E1 locus is largely unknown. Through positional cloning, we delimited the E1 locus to a 17.4-kb region containing an intron-free gene (E1). The E1 protein contains a putative bipartite nuclear localization signal and a region distantly related to B3 domain. In the recessive allele, a nonsynonymous substitution occurred in the putative nuclear localization signal, leading to the loss of localization specificity of the E1 protein and earlier flowering. The early-flowering phenotype was consistently observed in three ethylmethanesulfonate-induced mutants and two natural mutations that harbored a premature stop codon or a deletion of the entire E1 gene. E1 expression was significantly suppressed under short-day conditions and showed a bimodal diurnal pattern under long-day conditions, suggesting its response to photoperiod and its dominant effect induced by long day length. When a functional E1 gene was transformed into the early-flowering cultivar Kariyutaka with low E1 expression, transgenic plants carrying exogenous E1 displayed late flowering. Furthermore, the transcript abundance of E1 was negatively correlated with that of GmFT2a and GmFT5a, homologues of FLOWERING LOCUS T that promote flowering. These findings demonstrated the key role of E1 in repressing flowering and delaying maturity in soybean. The molecular identification of the maturity locus E1 will contribute to our understanding of the molecular mechanisms by which a short-day plant regulates flowering time and maturity.
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Affiliation(s)
- Zhengjun Xia
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Satoshi Watanabe
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Tetsuya Yamada
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yasutaka Tsubokura
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | | | - Hong Zhai
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Shusei Sato
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu 292-0812, Japan; and
| | - Toshimasa Yamazaki
- Biomolecular Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Shixiang Lü
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Hongyan Wu
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Satoshi Tabata
- Department of Plant Genome Research, Kazusa DNA Research Institute, Kisarazu 292-0812, Japan; and
| | - Kyuya Harada
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
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213
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Hayward A, Vighnesh G, Delay C, Samian MR, Manoli S, Stiller J, McKenzie M, Edwards D, Batley J. Second-generation sequencing for gene discovery in the Brassicaceae. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:750-759. [PMID: 22765874 DOI: 10.1111/j.1467-7652.2012.00719.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The Brassicaceae contains the most diverse collection of agriculturally important crop species of all plant families. Yet, this is one of the few families that do not form functional symbiotic associations with mycorrhizal fungi in the soil for improved nutrient acquisition. The genes involved in this symbiosis were more recently recruited by legumes for symbiotic association with nitrogen-fixing rhizobia bacteria. This study applied second-generation sequencing (SGS) and analysis tools to discover that two such genes, NSP1 (Nodulation Signalling Pathway 1) and NSP2, remain conserved in diverse members of the Brassicaceae despite the absence of these symbioses. We demonstrate the utility of SGS data for the discovery of putative gene homologs and their analysis in complex polyploid crop genomes with little prior sequence information. Furthermore, we show how this data can be applied to enhance downstream reverse genetics analyses. We hypothesize that Brassica NSP genes may function in the root in other plant-microbe interaction pathways that were recruited for mycorrhizal and rhizobial symbioses during evolution.
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Affiliation(s)
- Alice Hayward
- ARC Centre of Excellence for Integrative Legume Research, School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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214
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Development and characterization of a new TILLING population of common bread wheat (Triticum aestivum L.). PLoS One 2012; 7:e41570. [PMID: 22844501 PMCID: PMC3402408 DOI: 10.1371/journal.pone.0041570] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 06/28/2012] [Indexed: 12/04/2022] Open
Abstract
Mutagenesis is an important tool in crop improvement. However, the hexaploid genome of wheat (Triticum aestivum L.) presents problems in identifying desirable genetic changes based on phenotypic screening due to gene redundancy. TILLING (Targeting Induced Local Lesions IN Genomes), a powerful reverse genetic strategy that allows the detection of induced point mutations in individuals of the mutagenized populations, can address the major challenge of linking sequence information to the biological function of genes and can also identify novel variation for crop breeding. Wheat is especially well-suited for TILLING due to the high mutation densities tolerated by polyploids. However, only a few wheat TILLING populations are currently available in the world, which is far from satisfying the requirement of researchers and breeders in different growing environments. In addition, current TILLING screening protocols require costly fluorescence detection systems, limiting their use, especially in developing countries. We developed a new TILLING resource comprising 2610 M2 mutants in a common wheat cultivar ‘Jinmai 47’. Numerous phenotypes with altered morphological and agronomic traits were observed from the M2 and M3 lines in the field. To simplify the procedure and decrease costs, we use unlabeled primers and either non-denaturing polyacrylamide gels or agarose gels for mutation detection. The value of this new resource was tested using PCR with RAPD and Intron-spliced junction (ISJ) primers, and also TILLING in three selected candidate genes, in 300 and 512 mutant lines, revealing high mutation densities of 1/34 kb by RAPD/ISJ analysis and 1/47 kb by TILLING. In total, 31 novel alleles were identified in the 3 targeted genes and confirmed by sequencing. The results indicate that this mutant population represents a useful resource for the wheat research community. We hope that the use of this reverse genetics resource will provide novel allelic diversity for wheat improvement and functional genomics.
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215
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Bender R, Klinkenberg P, Jiang Z, Bauer B, Karypis G, Nguyen N, Perera MAD, Nikolau BJ, Carter CJ. Functional genomics of nectar production in the Brassicaceae. FLORA - MORPHOLOGY, DISTRIBUTION, FUNCTIONAL ECOLOGY OF PLANTS 2012. [PMID: 0 DOI: 10.1016/j.flora.2012.06.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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216
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Okabe Y, Asamizu E, Ariizumi T, Shirasawa K, Tabata S, Ezura H. Availability of Micro-Tom mutant library combined with TILLING in molecular breeding of tomato fruit shelf-life. BREEDING SCIENCE 2012; 62:202-8. [PMID: 23136532 PMCID: PMC3405968 DOI: 10.1270/jsbbs.62.202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 02/05/2012] [Indexed: 05/04/2023]
Abstract
Novel mutant alleles of an ethylene receptor Solanum lycopersicum ETHYLENE RESPONSE1 (SlETR1) gene, Sletr1-1 and Sletr1-2, were isolated from the Micro-Tom mutant library by TILLING in our previous study. They displayed different levels of impaired fruit ripening phenotype, suggesting that these alleles could be a valuable breeding material for improving shelf life of tomato fruit. To conduct practical use of the Sletr1 alleles in tomato breeding, genetic complementation analysis by transformation of genes carrying each allele is required. In this study, we generated and characterized transgenic lines over-expressing Sletr1-1 and Sletr1-2. All transgenic lines displayed ethylene insensitive phenotype and ripening inhibition, indicating that Sletr1-1 and Sletr1-2 associate with the ethylene insensitive phenotype. The level of ethylene sensitivity in the seedling was different between Sletr1-1 and Sletr1-2 transgenic lines, whereas no apparent difference was observed in fruit ripening phenotype. These results suggested that it is difficult to fine-tune the extent of ripening by transgenic approach even if the weaker allele (Sletr1-2) was used. Our present and previous studies indicate that the Micro-Tom mutant library combined with TILLING could be an efficient tool for exploring genetic variations of important agronomic traits in tomato breeding.
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Affiliation(s)
- Yoshihiro Okabe
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Erika Asamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Corresponding author (e-mail: )
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217
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Xu J, Liu Y, Liu J, Cao M, Wang J, Lan H, Xu Y, Lu Y, Pan G, Rong T. The genetic architecture of flowering time and photoperiod sensitivity in maize as revealed by QTL review and meta analysis. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2012; 54:358-73. [PMID: 22583799 DOI: 10.1111/j.1744-7909.2012.01128.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The control of flowering is not only important for reproduction, but also plays a key role in the processes of domestication and adaptation. To reveal the genetic architecture for flowering time and photoperiod sensitivity, a comprehensive evaluation of the relevant literature was performed and followed by meta analysis. A total of 25 synthetic consensus quantitative trait loci (QTL) and four hot-spot genomic regions were identified for photoperiod sensitivity including 11 genes related to photoperiod response or flower morphogenesis and development. Besides, a comparative analysis of the QTL for flowering time and photoperiod sensitivity highlighted the regions containing shared and unique QTL for the two traits. Candidate genes associated with maize flowering were identified through integrated analysis of the homologous genes for flowering time in plants and the consensus QTL regions for photoperiod sensitivity in maize (Zea mays L.). Our results suggest that the combination of literature review, meta-analysis and homologous blast is an efficient approach to identify new candidate genes and create a global view of the genetic architecture for maize photoperiodic flowering. Sequences of candidate genes can be used to develop molecular markers for various models of marker-assisted selection, such as marker-assisted recurrent selection and genomic selection that can contribute significantly to crop environmental adaptation.
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Affiliation(s)
- Jie Xu
- Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130, Sichuan, China
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218
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Re-orienting crop improvement for the changing climatic conditions of the 21st century. ACTA ACUST UNITED AC 2012. [DOI: 10.1186/2048-7010-1-7] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Abstract
A 70% increase in food production is required over the next four decades to feed an ever-increasing population. The inherent difficulties in achieving this unprecedented increase are exacerbated by the yield-depressing consequences of climate change and variations and by the pressures on food supply by other competing demographic and socioeconomic demands. With the dwindling or stagnant agricultural land and water resources, the sought-after increases will therefore be attained mainly through the enhancement of crop productivity under eco-efficient crop production systems. ‘Smart’ crop varieties that yield more with fewer inputs will be pivotal to success. Plant breeding must be re-oriented in order to generate these ‘smart’ crop varieties. This paper highlights some of the scientific and technological tools that ought to be the staple of all breeding programs. We also make the case that plant breeding must be enabled by adequate policies, including those that spur innovation and investments. To arrest and reverse the worrisome trend of declining capacities for crop improvement, a new generation of plant breeders must also be trained. Equally important, winning partnerships, including public-private sector synergies, are needed for 21st century plant breeding to bear fruits. We also urge the adoption of the continuum approach to the management of plant genetic resources for food and agriculture as means to improved cohesion of the components of its value chain. Compellingly also, the National Agricultural Research and Extension System of developing countries require comprehensive overhauling and strengthening as crop improvement and other interventions require a sustained platform to be effective. The development of a suite of actionable policy interventions to be packaged for assisting countries in developing result-oriented breeding programs is also called for.
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219
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Slade AJ, McGuire C, Loeffler D, Mullenberg J, Skinner W, Fazio G, Holm A, Brandt KM, Steine MN, Goodstal JF, Knauf VC. Development of high amylose wheat through TILLING. BMC PLANT BIOLOGY 2012; 12:69. [PMID: 22584013 PMCID: PMC3424102 DOI: 10.1186/1471-2229-12-69] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 05/14/2012] [Indexed: 05/19/2023]
Abstract
BACKGROUND Wheat (Triticum spp.) is an important source of food worldwide and the focus of considerable efforts to identify new combinations of genetic diversity for crop improvement. In particular, wheat starch composition is a major target for changes that could benefit human health. Starches with increased levels of amylose are of interest because of the correlation between higher amylose content and elevated levels of resistant starch, which has been shown to have beneficial effects on health for combating obesity and diabetes. TILLING (Targeting Induced Local Lesions in Genomes) is a means to identify novel genetic variation without the need for direct selection of phenotypes. RESULTS Using TILLING to identify novel genetic variation in each of the A and B genomes in tetraploid durum wheat and the A, B and D genomes in hexaploid bread wheat, we have identified mutations in the form of single nucleotide polymorphisms (SNPs) in starch branching enzyme IIa genes (SBEIIa). Combining these new alleles of SBEIIa through breeding resulted in the development of high amylose durum and bread wheat varieties containing 47-55% amylose and having elevated resistant starch levels compared to wild-type wheat. High amylose lines also had reduced expression of SBEIIa RNA, changes in starch granule morphology and altered starch granule protein profiles as evaluated by mass spectrometry. CONCLUSIONS We report the use of TILLING to develop new traits in crops with complex genomes without the use of transgenic modifications. Combined mutations in SBEIIa in durum and bread wheat varieties resulted in lines with significantly increased amylose and resistant starch contents.
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Affiliation(s)
- Ann J Slade
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - Cate McGuire
- Arcadia Biosciences, Inc, 202 Cousteau Pl, Suite 200, Davis, CA, 95618, USA
| | - Dayna Loeffler
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - Jessica Mullenberg
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - Wayne Skinner
- Arcadia Biosciences, Inc, 202 Cousteau Pl, Suite 200, Davis, CA, 95618, USA
| | - Gia Fazio
- Arcadia Biosciences, Inc, 202 Cousteau Pl, Suite 200, Davis, CA, 95618, USA
| | - Aaron Holm
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - Kali M Brandt
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - Michael N Steine
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
| | - John F Goodstal
- Arcadia Biosciences, Inc, 202 Cousteau Pl, Suite 200, Davis, CA, 95618, USA
| | - Vic C Knauf
- Arcadia Biosciences, Inc, 410 West Harrison St, Suite 150, Seattle, WA, 98119, USA
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220
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Lee DK, Van Norman JM, Murphy C, Adhikari E, Reed JW, Sieburth LE. In the absence of BYPASS1-related gene function, the bps signal disrupts embryogenesis by an auxin-independent mechanism. Development 2012; 139:805-15. [PMID: 22274700 DOI: 10.1242/dev.077313] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Development is often coordinated by biologically active mobile compounds that move between cells or organs. Arabidopsis mutants with defects in the BYPASS1 (BPS1) gene overproduce an active mobile compound that moves from the root to the shoot and inhibits growth. Here, we describe two related Arabidopsis genes, BPS2 and BPS3. Analyses of single, double and triple mutants revealed that all three genes regulate production of the same mobile compound, the bps signal, with BPS1 having the largest role. The triple mutant had a severe embryo defect, including the failure to properly establish provascular tissue, the shoot meristem and the root meristem. Aberrant expression of PINFORMED1, DR5, PLETHORA1, PLETHORA2 and WUSCHEL-LIKE HOMEOBOX5 were found in heart-stage bps triple-mutant embryos. However, auxin-induced gene expression, and localization of the PIN1 auxin efflux transporter, were intact in bps1 mutants, suggesting that the primary target of the bps signal is independent of auxin response. Thus, the bps signal identifies a novel signaling pathway that regulates patterning and growth in parallel with auxin signaling, in multiple tissues and at multiple developmental stages.
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Affiliation(s)
- Dong-Keun Lee
- Department of Biology, University of Utah, Salt Lake City, UT 94112, USA
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221
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Caroll D, Zhang B. Primer and interviews: advances in targeted gene modification. Interview by Julie C. Kiefer. Dev Dyn 2012; 240:2688-96. [PMID: 22072577 DOI: 10.1002/dvdy.22780] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Gene targeting in mice, first reported 25 years ago, has led to monumental advances in the understanding of basic biology and human disease. The ability to employ a similarly straightforward method for gene manipulation in other experimental organisms would make their already significant contributions all the more powerful. Here, we briefly outline the strengths and weaknesses of reverse genetics techniques in non-murine model organisms, ending with a more detailed description of two that promise to bring targeted gene modification to the masses: zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Dana Caroll, a forefather of zinc finger technology, and Bo Zhang, among the first to introduce TALEN-targeted mutagenesis to zebrafish, discuss their experience with these techniques, and speculate about the future of the field.
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Affiliation(s)
- Dana Caroll
- Department of Neurobiology and Anatomy, University of Utah, Salt Lake City, UT 84132, USA.
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222
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Gady ALF, Vriezen WH, Van de Wal MHBJ, Huang P, Bovy AG, Visser RGF, Bachem CWB. Induced point mutations in the phytoene synthase 1 gene cause differences in carotenoid content during tomato fruit ripening. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2012; 29:801-812. [PMID: 22408384 PMCID: PMC3285762 DOI: 10.1007/s11032-011-9591-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2011] [Accepted: 05/24/2011] [Indexed: 05/20/2023]
Abstract
In tomato, carotenoids are important with regard to major breeding traits such as fruit colour and human health. The enzyme phytoene synthase (PSY1) directs metabolic flux towards carotenoid synthesis. Through TILLING (Targeting Induced Local Lesions IN Genomes), we have identified two point mutations in the Psy1 gene. The first mutation is a knockout allele (W180*) and the second mutation leads to an amino acid substitution (P192L). Plants carrying the Psy1 knockout allele show fruit with a yellow flesh colour similar to the r, r mutant, with no further change in colour during ripening. In the line with P192L substitution, fruit remain yellow until 3 days post-breaker and eventually turn red. Metabolite profiling verified the absence of carotenoids in the W180* line and thereby confirms that PSY1 is the only enzyme introducing substrate into the carotenoid pathway in ripening fruit. More subtle effects on carotenoid accumulation were observed in the P192L line with a delay in lycopene and β-carotene accumulation clearly linked to a very slow synthesis of phytoene. The observation of lutein degradation with ripening in both lines showed that lutein and its precursors are still synthesised in ripening fruit. Gene expression analysis of key genes involved in carotenoid biosynthesis revealed that expression levels of genes in the pathway are not feedback-regulated by low levels or absence of carotenoid compounds. Furthermore, protein secondary structure modelling indicated that the P192L mutation affects PSY1 activity through misfolding, leading to the low phytoene accumulation.
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Affiliation(s)
- Antoine L. F. Gady
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Wim H. Vriezen
- Nunhems Netherlands BV, P.O. Box 4005, 6080 AA Haelen, The Netherlands
| | | | - Pingping Huang
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Graduate School Experimental Plant Sciences, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
- Present Address: Laboratory of Genetics, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Arnaud G. Bovy
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Richard G. F. Visser
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Christian W. B. Bachem
- Laboratory of Plant Breeding, Department of Plant Sciences, Wageningen-UR, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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223
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Fiume E, Fletcher JC. Regulation of Arabidopsis embryo and endosperm development by the polypeptide signaling molecule CLE8. THE PLANT CELL 2012; 24:1000-12. [PMID: 22427333 PMCID: PMC3336133 DOI: 10.1105/tpc.111.094839] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Revised: 02/07/2012] [Accepted: 02/26/2012] [Indexed: 05/19/2023]
Abstract
The plant seed is a major nutritional source for humans as well as an essential embryo development and dispersal unit. To ensure proper seed formation, fine spatial and temporal coordination between the embryo, endosperm, and maternal seed components must be achieved. However, the intercellular signaling pathways that direct the synchronous development of these tissues are poorly understood. Here we show that the Arabidopsis thaliana peptide ligand CLAVATA3/embryo surrounding region-related8 (CLE8) is exclusively expressed in young embryos and endosperm, and that it acts cell and noncell autonomously to regulate basal embryo cell division patterns, endosperm proliferation, and the timing of endosperm differentiation. CLE8 positively regulates expression of the transcription factor gene Wuschel-like homeobox8 (WOX8), and together CLE8 and WOX8 form a signaling module that promotes seed growth and overall seed size. These results demonstrate that seed development is coordinated by a secreted peptide ligand that plays a key early role in orchestrating cell patterning and proliferation in the embryo and endosperm.
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Affiliation(s)
- Elisa Fiume
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
| | - Jennifer C. Fletcher
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- Plant Gene Expression Center, U.S. Department of Agriculture–Agricultural Research Service/University of California, Albany, California 94710
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224
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Abu-Daya A, Khokha MK, Zimmerman LB. The hitchhiker's guide to Xenopus genetics. Genesis 2012; 50:164-75. [PMID: 22344745 DOI: 10.1002/dvg.22007] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 12/19/2011] [Accepted: 12/23/2011] [Indexed: 01/12/2023]
Abstract
A decade after the human genome sequence, most vertebrate gene functions remain poorly understood, limiting benefits to human health from rapidly advancing genomic technologies. Systematic in vivo functional analysis is ideally suited to the experimentally accessible Xenopus embryo, which combines embryological accessibility with a broad range of transgenic, biochemical, and gain-of-function assays. The diploid X. tropicalis adds loss-of-function genetics and enhanced genomics to this repertoire. In the last decade, diverse phenotypes have been recovered from genetic screens, mutations have been cloned, and reverse genetics in the form of TILLING and targeted gene editing have been established. Simple haploid genetics and gynogenesis and the very large number of embryos produced streamline screening and mapping. Improved genomic resources and the revolution in high-throughput sequencing are transforming mutation cloning and reverse genetic approaches. The combination of loss-of-function mutant backgrounds with the diverse array of conventional Xenopus assays offers a uniquely flexible platform for analysis of gene function in vertebrate development.
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Affiliation(s)
- Anita Abu-Daya
- Division of Developmental Biology, MRC-National Institute for Medical Research, Mill Hill, London, United Kingdom
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225
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Identification of rice transcription factors associated with drought tolerance using the Ecotilling method. PLoS One 2012; 7:e30765. [PMID: 22348023 PMCID: PMC3278407 DOI: 10.1371/journal.pone.0030765] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2011] [Accepted: 12/20/2011] [Indexed: 11/28/2022] Open
Abstract
The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the ‘line–source soil moisture gradient’, and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.
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226
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Guo S, Wagle M, Mathur P. Toward molecular genetic dissection of neural circuits for emotional and motivational behaviors. Dev Neurobiol 2012; 72:358-65. [DOI: 10.1002/dneu.20927] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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227
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Jegadeesan S, Yu K, Woodrow L, Wang Y, Shi C, Poysa V. Molecular analysis of glycinin genes in soybean mutants for development of gene-specific markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:365-72. [PMID: 21959908 DOI: 10.1007/s00122-011-1711-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 09/13/2011] [Indexed: 05/11/2023]
Abstract
Soybean mutant lines that differ in 11S glycinin and 7S β-conglycinin seed storage protein subunit compositions were developed. These proteins have significant influence on tofu quality. The molecular mechanisms underlying the mutant lines are unknown. In this study, gene-specific markers for five of the glycinin genes (Gy1 to Gy5) were developed using three 11S null lines, two A(4) null Japanese cultivars, Enrei and Raiden, and a control cultivar, Harovinton. Whereas gene-specific primers produced the appropriate products in the control cultivar for the Gy1, Gy2, Gy3 and Gy5 genes, they did not amplify in mutants missing the A(1a)B(2), A(2)B(1a), A(1b) B(1b), and A(3)B(4) subunits. However, ecotype targeting induced local lesions in genomes (EcoTILLING) and sequencing analysis revealed that the absence of the A(4) peptide in the mutants is due to the same point mutation as that in Enrei and Raiden. Selection efficiency of the gene-specific primer pairs was tested using a number of breeding lines segregating for the different subunits. Primer pairs specific to each of the Gy1, Gy2, Gy3, and Gy5 genes can be used to detect the presence or absence of amplification in normal or mutant lines. The Gy4 null allele can be selected for by temperature-switch PCR (TS-PCR) for identification of the A(4) (G4) null genotypes. In comparison to protein analysis by SDS-PAGE, gene-specific markers are easier, faster and more accurate for analysis, they do not have to use seed, and can be analyzed at any plant growth stage for marker-assisted selection.
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Affiliation(s)
- Souframanien Jegadeesan
- Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, 2585 County Road 20, Harrow, ON, N0R 1G0, Canada
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Marroni F, Pinosio S, Morgante M. The quest for rare variants: pooled multiplexed next generation sequencing in plants. FRONTIERS IN PLANT SCIENCE 2012; 3:133. [PMID: 22754557 PMCID: PMC3384946 DOI: 10.3389/fpls.2012.00133] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 06/04/2012] [Indexed: 05/08/2023]
Abstract
Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, few research groups working in plant sciences have exploited this potentiality, showing that pooled NGS provides results in excellent agreement with those obtained by individual Sanger sequencing. The aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method, we will explain in detail the possible experimental and analytical approaches and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled NGS can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity, and Tajima's D. Finally, we will discuss applications and future perspectives of the multiplexed NGS approach.
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Affiliation(s)
- Fabio Marroni
- Istituto di Genomica Applicata,Udine, Italy
- *Correspondence: Fabio Marroni, Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy. e-mail:
| | - Sara Pinosio
- Istituto di Genomica Applicata,Udine, Italy
- CNR, Istituto di Genetica Vegetale, Sezione di Firenze,Firenze, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata,Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, Università di Udine,Udine, Italy
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Braun N, de Saint Germain A, Pillot JP, Boutet-Mercey S, Dalmais M, Antoniadi I, Li X, Maia-Grondard A, Le Signor C, Bouteiller N, Luo D, Bendahmane A, Turnbull C, Rameau C. The pea TCP transcription factor PsBRC1 acts downstream of Strigolactones to control shoot branching. PLANT PHYSIOLOGY 2012; 158:225-38. [PMID: 22045922 PMCID: PMC3252107 DOI: 10.1104/pp.111.182725] [Citation(s) in RCA: 254] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 10/28/2011] [Indexed: 05/18/2023]
Abstract
The function of PsBRC1, the pea (Pisum sativum) homolog of the maize (Zea mays) TEOSINTE BRANCHED1 and the Arabidopsis (Arabidopsis thaliana) BRANCHED1 (AtBRC1) genes, was investigated. The pea Psbrc1 mutant displays an increased shoot-branching phenotype, is able to synthesize strigolactone (SL), and does not respond to SL application. The level of pleiotropy of the SL-deficient ramosus1 (rms1) mutant is higher than in the Psbrc1 mutant, rms1 exhibiting a relatively dwarf phenotype and more extensive branching at upper nodes. The PsBRC1 gene is mostly expressed in the axillary bud and is transcriptionally up-regulated by direct application of the synthetic SL GR24 and down-regulated by the cytokinin (CK) 6-benzylaminopurine. The results suggest that PsBRC1 may have a role in integrating SL and CK signals and that SLs act directly within the bud to regulate its outgrowth. However, the Psbrc1 mutant responds to 6-benzylaminopurine application and decapitation by increasing axillary bud length, implicating a PsBRC1-independent component of the CK response in sustained bud growth. In contrast to other SL-related mutants, the Psbrc1 mutation does not cause a decrease in the CK zeatin riboside in the xylem sap or a strong increase in RMS1 transcript levels, suggesting that the RMS2-dependent feedback is not activated in this mutant. Surprisingly, the double rms1 Psbrc1 mutant displays a strong increase in numbers of branches at cotyledonary nodes, whereas branching at upper nodes is not significantly higher than the branching in rms1. This phenotype indicates a localized regulation of branching at these nodes specific to pea.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Catherine Rameau
- Institut Jean-Pierre Bourgin, INRA UMR1318 INRA-AgroParisTech, F–78000 Versailles, France (N. Braun, A.d.S.G., J.-P.P., S.B.-M., A.M.-G., C.R.); School of Life Sciences, Sun Yat Sen University, Guangzhou 510275, China (X.L., D.L.); Unité de Recherche en Génomique Végétale, INRA/CNRS, 91057 Evry cedex, France (M.D., N. Bouteiller, A.B.); INRA Dijon, 21065 Dijon cedex, France (C.L.S.); Division of Cell and Molecular Biology, Imperial College London, London SW7 2AZ, United Kingdom (I.A., C.T.)
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Lidder P, Sonnino A. Biotechnologies for the management of genetic resources for food and agriculture. ADVANCES IN GENETICS 2012; 78:1-167. [PMID: 22980921 DOI: 10.1016/b978-0-12-394394-1.00001-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.
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Affiliation(s)
- Preetmoninder Lidder
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
| | - Andrea Sonnino
- Office of Knowledge Exchange, Research and Extension, Research and Extension Branch, Food and Agriculture Organization of the UN (FAO), Viale delle Terme di Caracalla, Rome, Italy
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Mazier M, Flamain F, Nicolaï M, Sarnette V, Caranta C. Knock-down of both eIF4E1 and eIF4E2 genes confers broad-spectrum resistance against potyviruses in tomato. PLoS One 2011; 6:e29595. [PMID: 22242134 PMCID: PMC3248445 DOI: 10.1371/journal.pone.0029595] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/01/2011] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The eukaryotic translation initiation factor eIF4E plays a key role in plant-potyvirus interactions. eIF4E belongs to a small multigenic family and three genes, eIF4E1, eIF4E2 and eIF(iso)4E, have been identified in tomato. It has been demonstrated that eIF4E-mediated natural recessive resistances against potyviruses result from non-synonymous mutations in an eIF4E protein, which impair its direct interaction with the potyviral protein VPg. In tomato, the role of eIF4E proteins in potyvirus resistance is still unclear because natural or induced mutations in eIF4E1 confer only a narrow resistance spectrum against potyviruses. This contrasts with the broad spectrum resistance identified in the natural diversity of tomato. These results suggest that more than one eIF4E protein form is involved in the observed broad spectrum resistance. METHODOLOGY/PRINCIPAL FINDINGS To gain insight into the respective contribution of each eIF4E protein in tomato-potyvirus interactions, two tomato lines silenced for both eIF4E1 and eIF4E2 (RNAi-4E) and two lines silenced for eIF(iso)4E (RNAi-iso4E) were obtained and characterized. RNAi-4E lines are slightly impaired in their growth and fertility, whereas no obvious growth defects were observed in RNAi-iso4E lines. The F1 hybrid between RNAi-4E and RNAi-iso4E lines presented a pronounced semi-dwarf phenotype. Interestingly, the RNAi-4E lines silenced for both eIF4E1 and eIF4E2 showed broad spectrum resistance to potyviruses while the RNAi-iso4E lines were fully susceptible to potyviruses. Yeast two-hybrid interaction assays between the three eIF4E proteins and a set of viral VPgs identified two types of VPgs: those that interacted only with eIF4E1 and those that interacted with either eIF4E1 or with eIF4E2. CONCLUSION/SIGNIFICANCE These experiments provide evidence for the involvement of both eIF4E1 and eIF4E2 in broad spectrum resistance of tomato against potyviruses and suggest a role for eIF4E2 in tomato-potyvirus interactions.
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Affiliation(s)
- Marianne Mazier
- Unité de Génétique et Amélioration des Fruits et Légumes, INRA, UR1052, Montfavet, France.
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Lochlainn SÓ, Amoah S, Graham NS, Alamer K, Rios JJ, Kurup S, Stoute A, Hammond JP, Østergaard L, King GJ, White PJ, Broadley MR. High Resolution Melt (HRM) analysis is an efficient tool to genotype EMS mutants in complex crop genomes. PLANT METHODS 2011; 7:43. [PMID: 22152063 PMCID: PMC3251530 DOI: 10.1186/1746-4811-7-43] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/08/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Targeted Induced Loci Lesions IN Genomes (TILLING) is increasingly being used to generate and identify mutations in target genes of crop genomes. TILLING populations of several thousand lines have been generated in a number of crop species including Brassica rapa. Genetic analysis of mutants identified by TILLING requires an efficient, high-throughput and cost effective genotyping method to track the mutations through numerous generations. High resolution melt (HRM) analysis has been used in a number of systems to identify single nucleotide polymorphisms (SNPs) and insertion/deletions (IN/DELs) enabling the genotyping of different types of samples. HRM is ideally suited to high-throughput genotyping of multiple TILLING mutants in complex crop genomes. To date it has been used to identify mutants and genotype single mutations. The aim of this study was to determine if HRM can facilitate downstream analysis of multiple mutant lines identified by TILLING in order to characterise allelic series of EMS induced mutations in target genes across a number of generations in complex crop genomes. RESULTS We demonstrate that HRM can be used to genotype allelic series of mutations in two genes, BraA.CAX1a and BraA.MET1.a in Brassica rapa. We analysed 12 mutations in BraA.CAX1.a and five in BraA.MET1.a over two generations including a back-cross to the wild-type. Using a commercially available HRM kit and the Lightscanner™ system we were able to detect mutations in heterozygous and homozygous states for both genes. CONCLUSIONS Using HRM genotyping on TILLING derived mutants, it is possible to generate an allelic series of mutations within multiple target genes rapidly. Lines suitable for phenotypic analysis can be isolated approximately 8-9 months (3 generations) from receiving M3 seed of Brassica rapa from the RevGenUK TILLING service.
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Affiliation(s)
- Seosamh Ó Lochlainn
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | - Neil S Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Khalid Alamer
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Juan J Rios
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | | | | | - John P Hammond
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Lars Østergaard
- Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, PO Box 157Lismore NSW 2480, Australia
| | - Phillip J White
- The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
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Botticella E, Sestili F, Hernandez-Lopez A, Phillips A, Lafiandra D. High resolution melting analysis for the detection of EMS induced mutations in wheat SBEIIa genes. BMC PLANT BIOLOGY 2011; 11:156. [PMID: 22074448 PMCID: PMC3228712 DOI: 10.1186/1471-2229-11-156] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Accepted: 11/10/2011] [Indexed: 05/20/2023]
Abstract
BACKGROUND Manipulation of the amylose-amylopectin ratio in cereal starch has been identified as a major target for the production of starches with novel functional properties. In wheat, silencing of starch branching enzyme genes by a transgenic approach reportedly caused an increase of amylose content up to 70% of total starch, exhibiting novel and interesting nutritional characteristics. In this work, the functionality of starch branching enzyme IIa (SBEIIa) has been targeted in bread wheat by TILLING. An EMS-mutagenised wheat population has been screened using High Resolution Melting of PCR products to identify functional SNPs in the three homoeologous genes encoding the target enzyme in the hexaploid genome. RESULTS This analysis resulted in the identification of 56, 14 and 53 new allelic variants respectively for SBEIIa-A, SBEIIa-B and SBEIIa-D. The effects of the mutations on protein structure and functionality were evaluated by a bioinformatic approach. Two putative null alleles containing non-sense or splice site mutations were identified for each of the three homoeologous SBEIIa genes; qRT-PCR analysis showed a significant decrease of their gene expression and resulted in increased amylose content. Pyramiding of different single null homoeologous allowed to isolate double null mutants showing an increase of amylose content up to 21% compared to the control. CONCLUSION TILLING has successfully been used to generate novel alleles for SBEIIa genes known to control amylose content in wheat. Single and double null SBEIIa genotypes have been found to show a significant increase in amylose content.
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Affiliation(s)
- Ermelinda Botticella
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
| | - Francesco Sestili
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
| | | | - Andrew Phillips
- Plant Science Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Domenico Lafiandra
- Department of Agriculture, Forests, Nature and Energy, University of Tuscia, 01100 Viterbo, Italy
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Su SH, Clark KA, Gibbs NM, Bush SM, Krysan PJ. Ice-Cap: a method for growing Arabidopsis and tomato plants in 96-well plates for high-throughput genotyping. J Vis Exp 2011:3280. [PMID: 22105217 PMCID: PMC3308595 DOI: 10.3791/3280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
It is becoming common for plant scientists to develop projects that require the genotyping of large numbers of plants. The first step in any genotyping project is to collect a tissue sample from each individual plant. The traditional approach to this task is to sample plants one-at-a-time. If one wishes to genotype hundreds or thousands of individuals, however, using this strategy results in a significant bottleneck in the genotyping pipeline. The Ice-Cap method that we describe here provides a high-throughput solution to this challenge by allowing one scientist to collect tissue from several thousand seedlings in a single day 1,2. This level of throughput is made possible by the fact that tissue is harvested from plants 96-at-a-time, rather than one-at-a-time. The Ice-Cap method provides an integrated platform for performing seedling growth, tissue harvest, and DNA extraction. The basis for Ice-Cap is the growth of seedlings in a stacked pair of 96-well plates. The wells of the upper plate contain plugs of agar growth media on which individual seedlings germinate. The roots grow down through the agar media, exit the upper plate through a hole, and pass into a lower plate containing water. To harvest tissue for DNA extraction, the water in the lower plate containing root tissue is rapidly frozen while the seedlings in the upper plate remain at room temperature. The upper plate is then peeled away from the lower plate, yielding one plate with 96 root tissue samples frozen in ice and one plate with 96 viable seedlings. The technique is named "Ice-Cap" because it uses ice to capture the root tissue. The 96-well plate containing the seedlings can then wrapped in foil and transferred to low temperature. This process suspends further growth of the seedlings, but does not affect their viability. Once genotype analysis has been completed, seedlings with the desired genotype can be transferred from the 96-well plate to soil for further propagation. We have demonstrated the utility of the Ice-Cap method using Arabidopsis thaliana, tomato, and rice seedlings. We expect that the method should also be applicable to other species of plants with seeds small enough to fit into the wells of 96-well plates.
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Affiliation(s)
- Shih-Heng Su
- Horticulture Department, University of Wisconsin-Madison, USA
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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Okabe Y, Asamizu E, Saito T, Matsukura C, Ariizumi T, Brès C, Rothan C, Mizoguchi T, Ezura H. Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. PLANT & CELL PHYSIOLOGY 2011; 52:1994-2005. [PMID: 21965606 PMCID: PMC3212723 DOI: 10.1093/pcp/pcr134] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Accepted: 09/26/2011] [Indexed: 05/19/2023]
Abstract
To accelerate functional genomic research in tomato, we developed a Micro-Tom TILLING (Targeting Induced Local Lesions In Genomes) platform. DNA pools were constructed from 3,052 ethyl methanesulfonate (EMS) mutant lines treated with 0.5 or 1.0% EMS. The mutation frequency was calculated by screening 10 genes. The 0.5% EMS population had a mild mutation frequency of one mutation per 1,710 kb, whereas the 1.0% EMS population had a frequency of one mutation per 737 kb, a frequency suitable for producing an allelic series of mutations in the target genes. The overall mutation frequency was one mutation per 1,237 kb, which affected an average of three alleles per kilobase screened. To assess whether a Micro-Tom TILLING platform could be used for efficient mutant isolation, six ethylene receptor genes in tomato (SlETR1-SlETR6) were screened. Two allelic mutants of SlETR1 (Sletr1-1 and Sletr1-2) that resulted in reduced ethylene responses were identified, indicating that our Micro-Tom TILLING platform provides a powerful tool for the rapid detection of mutations in an EMS mutant library. This work provides a practical and publicly accessible tool for the study of fruit biology and for obtaining novel genetic material that can be used to improve important agronomic traits in tomato.
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Affiliation(s)
- Yoshihiro Okabe
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Erika Asamizu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Takeshi Saito
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Chiaki Matsukura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Cécile Brès
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Christophe Rothan
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
- Univ. Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140 Villenave d'Ornon, France
| | - Tsuyoshi Mizoguchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572 Japan
- *Corresponding author: E-mail, ; Fax, +81-29-853-7734
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Kurowska M, Daszkowska-Golec A, Gruszka D, Marzec M, Szurman M, Szarejko I, Maluszynski M. TILLING: a shortcut in functional genomics. J Appl Genet 2011; 52:371-90. [PMID: 21912935 PMCID: PMC3189332 DOI: 10.1007/s13353-011-0061-1] [Citation(s) in RCA: 96] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 08/16/2011] [Accepted: 08/17/2011] [Indexed: 11/01/2022]
Abstract
Recent advances in large-scale genome sequencing projects have opened up new possibilities for the application of conventional mutation techniques in not only forward but also reverse genetics strategies. TILLING (Targeting Induced Local Lesions IN Genomes) was developed a decade ago as an alternative to insertional mutagenesis. It takes advantage of classical mutagenesis, sequence availability and high-throughput screening for nucleotide polymorphisms in a targeted sequence. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of its genome size and ploidy level. The TILLING protocol provides a high frequency of point mutations distributed randomly in the genome. The great mutagenic potential of chemical agents to generate a high rate of nucleotide substitutions has been proven by the high density of mutations reported for TILLING populations in various plant species. For most of them, the analysis of several genes revealed 1 mutation/200-500 kb screened and much higher densities were observed for polyploid species, such as wheat. High-throughput TILLING permits the rapid and low-cost discovery of new alleles that are induced in plants. Several research centres have established a TILLING public service for various plant species. The recent trends in TILLING procedures rely on the diversification of bioinformatic tools, new methods of mutation detection, including mismatch-specific and sensitive endonucleases, but also various alternatives for LI-COR screening and single nucleotide polymorphism (SNP) discovery using next-generation sequencing technologies. The TILLING strategy has found numerous applications in functional genomics. Additionally, wide applications of this throughput method in basic and applied research have already been implemented through modifications of the original TILLING strategy, such as Ecotilling or Deletion TILLING.
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Affiliation(s)
- Marzena Kurowska
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Agata Daszkowska-Golec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Damian Gruszka
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Marek Marzec
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miriam Szurman
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Iwona Szarejko
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
| | - Miroslaw Maluszynski
- Department of Genetics, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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Dolferus R, Ji X, Richards RA. Abiotic stress and control of grain number in cereals. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:331-41. [PMID: 21889038 DOI: 10.1016/j.plantsci.2011.05.015] [Citation(s) in RCA: 123] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 05/26/2011] [Accepted: 05/26/2011] [Indexed: 05/18/2023]
Abstract
Grain number is the only yield component that is directly associated with increased grain yield in important cereal crops like wheat. Historical yield studies show that increases in grain yield are always accompanied by an increase in grain number. Adverse weather conditions can cause severe fluctuations in grain yield and substantial yield losses in cereal crops. The problem is global and despite its impact on world food production breeding and selection approaches have only met with limited success. A specific period during early reproductive development, the young microspore stage of pollen development, is extremely vulnerable to abiotic stress in self-fertilising cereals (wheat, rice, barley, sorghum). A better understanding of the physiological and molecular processes that lead to stress-induced pollen abortion may provide us with the key to finding solutions for maintaining grain number under abiotic stress conditions. Due to the complexity of the problem, stress-proofing our main cereal crops will be a challenging task and will require joint input from different research disciplines.
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Affiliation(s)
- Rudy Dolferus
- CSIRO Plant Industry, Canberra, ACT 2601, Australia.
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Busch BL, Schmitz G, Rossmann S, Piron F, Ding J, Bendahmane A, Theres K. Shoot branching and leaf dissection in tomato are regulated by homologous gene modules. THE PLANT CELL 2011; 23:3595-609. [PMID: 22039213 PMCID: PMC3229137 DOI: 10.1105/tpc.111.087981] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/19/2011] [Accepted: 10/17/2011] [Indexed: 05/18/2023]
Abstract
Aerial plant architecture is predominantly determined by shoot branching and leaf morphology, which are governed by apparently unrelated developmental processes, axillary meristem formation, and leaf dissection. Here, we show that in tomato (Solanum lycopersicum), these processes share essential functions in boundary establishment. Potato leaf (C), a key regulator of leaf dissection, was identified to be the closest paralog of the shoot branching regulator Blind (Bl). Comparative genomics revealed that these two R2R3 MYB genes are orthologs of the Arabidopsis thaliana branching regulator REGULATOR OF AXILLARY MERISTEMS1 (RAX1). Expression studies and complementation analyses indicate that these genes have undergone sub- or neofunctionalization due to promoter differentiation. C acts in a pathway independent of other identified leaf dissection regulators. Furthermore, the known leaf complexity regulator Goblet (Gob) is crucial for axillary meristem initiation and acts in parallel to C and Bl. Finally, RNA in situ hybridization revealed that the branching regulator Lateral suppressor (Ls) is also expressed in leaves. All four boundary genes, C, Bl, Gob, and Ls, may act by suppressing growth, as indicated by gain-of-function plants. Thus, leaf architecture and shoot architecture rely on a conserved mechanism of boundary formation preceding the initiation of leaflets and axillary meristems.
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Affiliation(s)
- Bernhard L. Busch
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Gregor Schmitz
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Susanne Rossmann
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Florence Piron
- Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 91057 Evry cedex, France
| | - Jia Ding
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
| | - Abdelhafid Bendahmane
- Unité de Recherche en Génomique Végétale, Unité Mixte de Recherche, Institut National de la Recherche Agronomique–Centre National de la Recherche Scientifique, 91057 Evry cedex, France
| | - Klaus Theres
- Max Planck Institute for Plant Breeding Research, 50829 Cologne, Germany
- Address correspondence to
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Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, Gu Y, Hazen SP, Holt BF, Hong SY, Jordan M, Manzaneda AJ, Mitchell-Olds T, Mochida K, Mur LA, Park CM, Sedbrook J, Watt M, Zheng SJ, Vogel JP. Brachypodium as a model for the grasses: today and the future. PLANT PHYSIOLOGY 2011; 157:3-13. [PMID: 21771916 PMCID: PMC3165879 DOI: 10.1104/pp.111.179531] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Accepted: 07/18/2011] [Indexed: 05/06/2023]
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - John P. Vogel
- Plant Biotechnology Center and Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210 (J.B., E.G., R.S.); Department of Botany and Plant Pathology and Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331 (T.M.); United States Department of Agriculture-Agricultural Research Service Plant Science Research Unit and Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 (D.F.G.); Crop Genetics Department (P.V.) and Cell and Developmental Biology Department (M.B.), John Innes Centre, Norwich NR4 7UJ, United Kingdom; Boyce Thompson Institute, Ithaca, New York 14853 (T.B.); Institut Jean-Pierre Bourgin, UMR1318 Institut National de la Recherche Agronomique-AgroParisTech, Versailles 78026, France (R.S.); Faculty of Engineering and Natural Science, Sabanci University, Istanbul 34956, Turkey (H.B.); Biology Department, University of Massachusetts, Amherst, Massachusetts 01003 (A.L.C., S.P.H.); State Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (C.G.); Genomics and Gene Discovery Research Unit, United States Department of Agriculture-Agricultural Research Service Western Regional Research Center, Albany, California 94710 (Y.G., J.P.V.); Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019 (B.F.H.); Department of Chemistry, Seoul National University, Seoul 151–742 Korea (S.-Y.H., C.-M.P.); Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, Manitoba, Canada R3T 2M9 (M.J.); Departamento de Biología Animal, Biología Vegetal y Ecología, Universidad de Jaén, Jaen 23071 Spain (A.J.M.); Institute for Genome Sciences and Policy, Department of Biology, Duke University, Durham, North Carolina 27708 (T.M.-O.); RIKEN Biomass Engineering Program, RIKEN Plant Science Center, Kanagawa 230–0045, Japan (K.M.); Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales SY23 3DA, United Kingdom (L.A.J.M.); School of Biological Sciences, Illinois State University and Department of Energy Great Lakes Bioenergy Research Center, Normal, Illinois 61790 (J.S.); CSIRO Plant Industry, Canberra, Australian Capital Territory 2601, Australia (M.W.); College of Life Sciences, Zhejiang University, Hangzhou 310058, China (S.J.Z.)
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Carelli M, Biazzi E, Panara F, Tava A, Scaramelli L, Porceddu A, Graham N, Odoardi M, Piano E, Arcioni S, May S, Scotti C, Calderini O. Medicago truncatula CYP716A12 Is a Multifunctional Oxidase Involved in the Biosynthesis of Hemolytic Saponins. THE PLANT CELL 2011; 23:3070-81. [PMID: 21821776 PMCID: PMC3180811 DOI: 10.1105/tpc.111.087312] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Abstract
Saponins, a group of glycosidic compounds present in several plant species, have aglycone moieties that are formed using triterpenoid or steroidal skeletons. In spite of their importance as antimicrobial compounds and their possible benefits for human health, knowledge of the genetic control of saponin biosynthesis is still poorly understood. In the Medicago genus, the hemolytic activity of saponins is related to the nature of their aglycone moieties. We have identified a cytochrome P450 gene (CYP716A12) involved in saponin synthesis in Medicago truncatula using a combined genetic and biochemical approach. Genetic loss-of-function analysis and complementation studies showed that CYP716A12 is responsible for an early step in the saponin biosynthetic pathway. Mutants in CYP716A12 were unable to produce hemolytic saponins and only synthetized soyasaponins, and were thus named lacking hemolytic activity (lha). In vitro enzymatic activity assays indicate that CYP716A12 catalyzes the oxidation of β-amyrin and erythrodiol at the C-28 position, yielding oleanolic acid. Transcriptome changes in the lha mutant showed a modulation in the main steps of triterpenic saponin biosynthetic pathway: squalene cyclization, β-amyrin oxidation, and glycosylation. The analysis of CYP716A12 expression in planta is reported together with the sapogenin content in different tissues and stages. This article provides evidence for CYP716A12 being a key gene in hemolytic saponin biosynthesis.
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Affiliation(s)
- Maria Carelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Elisa Biazzi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Francesco Panara
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Aldo Tava
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Laura Scaramelli
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Andrea Porceddu
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Neil Graham
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Miriam Odoardi
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Efisio Piano
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Sergio Arcioni
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
| | - Sean May
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Carla Scotti
- Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per le Produzioni Foraggere e Lattiero-Casearie, 26900 Lodi, Italy
| | - Ornella Calderini
- Consiglio Nazionale delle Ricerche (CNR)-Istituto di Genetica Vegetale (IGV), 06128 Perugia, Italy
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243
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Missirian V, Comai L, Filkov V. Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics 2011. [PMID: 21756356 DOI: 10.1186/1471‐2105‐12‐287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND TILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals. Combined with the high-throughput of next-generation sequencing technologies, and the resolving power of overlapping pool design, TILLING provides an efficient and economical platform for functional genomics across thousands of organisms. RESULTS We propose a probabilistic method for calling TILLING-induced mutations, and their carriers, from high throughput sequencing data of overlapping population pools, where each individual occurs in two pools. We assign a probability score to each sequence position by applying Bayes' Theorem to a simplified binomial model of sequencing error and expected mutations, taking into account the coverage level. We test the performance of our method on variable quality, high-throughput sequences from wheat and rice mutagenized populations. CONCLUSIONS We show that our method effectively discovers mutations in large populations with sensitivity of 92.5% and specificity of 99.8%. It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data. The implementation of our method is available from: http://www.cs.ucdavis.edu/filkov/CAMBa/.
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Affiliation(s)
- Victor Missirian
- Department of Computer Science, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
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244
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Barkley NA, Wang ML. Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals. Curr Genomics 2011; 9:212-26. [PMID: 19452039 PMCID: PMC2682938 DOI: 10.2174/138920208784533656] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 04/24/2008] [Accepted: 04/28/2008] [Indexed: 11/22/2022] Open
Abstract
With the fairly recent advent of inexpensive, rapid sequencing technologies that continue to improve sequencing efficiency and accuracy, many species of animals, plants, and microbes have annotated genomic information publicly available. The focus on genomics has thus been shifting from the collection of whole sequenced genomes to the study of functional genomics. Reverse genetic approaches have been used for many years to advance from sequence data to the resulting phenotype in an effort to deduce the function of a gene in the species of interest. Many of the currently used approaches (RNAi, gene knockout, site-directed mutagenesis, transposon tagging) rely on the creation of transgenic material, the development of which is not always feasible for many plant or animal species. TILLING is a non-transgenic reverse genetics approach that is applicable to all animal and plant species which can be mutagenized, regardless of its mating / pollinating system, ploidy level, or genome size. This approach requires prior DNA sequence information and takes advantage of a mismatch endonuclease to locate and detect induced mutations. Ultimately, it can provide an allelic series of silent, missense, nonsense, and splice site mutations to examine the effect of various mutations in a gene. TILLING has proven to be a practical, efficient, and an effective approach for functional genomic studies in numerous plant and animal species. EcoTILLING, which is a variant of TILLING, examines natural genetic variation in populations and has been successfully utilized in animals and plants to discover SNPs including rare ones. In this review, TILLING and EcoTILLING techniques, beneficial applications and limitations from plant and animal studies are discussed.
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Affiliation(s)
- N A Barkley
- USDA-ARS, Plant Genetic Resources Conservation Unit (PGRCU), 1109 Experiment Street, Griffin, GA 30223, USA
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245
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Missirian V, Comai L, Filkov V. Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments. BMC Bioinformatics 2011; 12:287. [PMID: 21756356 PMCID: PMC3150297 DOI: 10.1186/1471-2105-12-287] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 07/14/2011] [Indexed: 11/17/2022] Open
Abstract
Background TILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals. Combined with the high-throughput of next-generation sequencing technologies, and the resolving power of overlapping pool design, TILLING provides an efficient and economical platform for functional genomics across thousands of organisms. Results We propose a probabilistic method for calling TILLING-induced mutations, and their carriers, from high throughput sequencing data of overlapping population pools, where each individual occurs in two pools. We assign a probability score to each sequence position by applying Bayes' Theorem to a simplified binomial model of sequencing error and expected mutations, taking into account the coverage level. We test the performance of our method on variable quality, high-throughput sequences from wheat and rice mutagenized populations. Conclusions We show that our method effectively discovers mutations in large populations with sensitivity of 92.5% and specificity of 99.8%. It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data. The implementation of our method is available from: http://www.cs.ucdavis.edu/filkov/CAMBa/.
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Affiliation(s)
- Victor Missirian
- Department of Computer Science, UC Davis, 1 Shields Ave., Davis, CA 95616, USA
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246
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Sabetta W, Alba V, Blanco A, Montemurro C. sunTILL: a TILLING resource for gene function analysis in sunflower. PLANT METHODS 2011; 7:20. [PMID: 21718494 PMCID: PMC3169506 DOI: 10.1186/1746-4811-7-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2011] [Accepted: 06/30/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND Cultivated sunflower (Helianthus annus L.) is a globally important oilseed crop, subjected to intensive genetic and genomic studies. Although classical mutagenesis has successfully been applied to Helianthus genus in the past, we have developed the first sunflower TILLING resource. RESULTS To balance the maximum mutation density with an acceptable plant survival rate, a 'kill curve' analysis was first conducted with different ethylmethanesulfonate (EMS) dosages and different exposure times. According to the germination rate, a treatment with 0.7% EMS for 6 h was chosen. An M2 progeny of 3,651 fertile plants was obtained. Totally, 4.79% of the whole population showed clear aberrant phenotypes. A microsatellite analysis on a representative sample of the original seed stock and mutant lines confirmed the uniformity of the genetic background of plant material. The TILLING procedure was successfully applied to sunflower genome, initially by a CelI-nuclease mismatch cleavage assay coupled with a DNA-pooling level test. To investigate the efficiency of the mutagenic treatment, a pilot screening was carried out on 1,152 M2 lines focusing on four genes, three involved in the fatty acid biosynthetic pathway and one for downy mildew resistance. A total of 9 mutant lines were identified and confirmed by sequencing; thereby, the estimated overall mutation frequency for the pilot assay resulted to be 1/475 kb. CONCLUSION A first TILLING population for a high throughput identification of EMS-induced point mutations in sunflower genome has been successfully obtained. This represents a powerful tool to a better understanding of gene function in sunflower.
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Affiliation(s)
- Wilma Sabetta
- Department of Agro-Forestry and Environmental Biology and Chemistry, Section of Genetics and Breeding, University of Bari, via Amendola 165/A, 70126, Bari, Italy
| | - Vittorio Alba
- Department of Agro-Forestry and Environmental Biology and Chemistry, Section of Genetics and Breeding, University of Bari, via Amendola 165/A, 70126, Bari, Italy
| | - Antonio Blanco
- Department of Agro-Forestry and Environmental Biology and Chemistry, Section of Genetics and Breeding, University of Bari, via Amendola 165/A, 70126, Bari, Italy
| | - Cinzia Montemurro
- Department of Agro-Forestry and Environmental Biology and Chemistry, Section of Genetics and Breeding, University of Bari, via Amendola 165/A, 70126, Bari, Italy
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247
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Monfared MM, Simon MK, Meister RJ, Roig-Villanova I, Kooiker M, Colombo L, Fletcher JC, Gasser CS. Overlapping and antagonistic activities of BASIC PENTACYSTEINE genes affect a range of developmental processes in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:1020-31. [PMID: 21435046 DOI: 10.1111/j.1365-313x.2011.04562.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The BASIC PENTACYSTEINE (BPC) proteins are a plant-specific transcription factor family that is present throughout land plants. The Arabidopsis BPC proteins have been categorized into three classes based on sequence similarity, and we demonstrate that there is functional overlap between classes. Single gene mutations produce no visible phenotypic effects, and severe morphological phenotypes occur only in higher order mutants between members of classes I and II, with the most severe phenotype observed in bpc1-1 bpc2 bpc4 bpc6 plants. These quadruple mutants are dwarfed and display small curled leaves, aberrant ovules, altered epidermal cells and reduced numbers of lateral roots. Affected processes include coordinated growth of cell layers, cell shape determination and timing of senescence. Disruption of BPC3 function rescues some aspects of the bpc1-1 bpc2 bpc4 bpc6 phenotype, indicating that BPC3 function may be antagonistic to other members of the family. Ethylene response is diminished in bpc1-1 bpc2 bpc4 bpc6 plants, although not all aspects of the phenotype can be explained by reduced ethylene sensitivity. Our data indicate that the BPC transcription factor family is integral for a wide range of processes that support normal growth and development.
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Affiliation(s)
- Mona M Monfared
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
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248
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Candela H, Pérez-Pérez JM, Micol JL. Uncovering the post-embryonic functions of gametophytic- and embryonic-lethal genes. TRENDS IN PLANT SCIENCE 2011; 16:336-345. [PMID: 21420345 DOI: 10.1016/j.tplants.2011.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 02/09/2011] [Accepted: 02/17/2011] [Indexed: 05/30/2023]
Abstract
An estimated 500-1 000 Arabidopsis (Arabidopsis thaliana) genes mutate to embryonic lethality. In addition, several hundred mutations have been identified that cause gametophytic lethality. Thus, a significant fraction of the ∼25,000 protein-coding genes in Arabidopsis are indispensable to the early stages of the diploid phase or to the haploid gametophytic phase. The expression patterns of many of these genes indicate that they also act later in development but, because the mutants die at such early stages, conventional methods limit the study of their roles in adult diploid plants. Here, we describe the toolset that allows researchers to assess the post-embryonic functions of plant genes for which only gametophytic- and embryonic-lethal alleles have been isolated.
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Affiliation(s)
- Héctor Candela
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Alicante, Spain
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249
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Watanabe S, Xia Z, Hideshima R, Tsubokura Y, Sato S, Yamanaka N, Takahashi R, Anai T, Tabata S, Kitamura K, Harada K. A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering. Genetics 2011; 188:395-407. [PMID: 21406680 PMCID: PMC3122305 DOI: 10.1534/genetics.110.125062] [Citation(s) in RCA: 250] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/03/2011] [Indexed: 12/17/2022] Open
Abstract
Flowering is indicative of the transition from vegetative to reproductive phase, a critical event in the life cycle of plants. In soybean (Glycine max), a flowering quantitative trait locus, FT2, corresponding to the maturity locus E2, was detected in recombinant inbred lines (RILs) derived from the varieties "Misuzudaizu" (ft2/ft2; JP28856) and "Moshidou Gong 503" (FT2/FT2; JP27603). A map-based cloning strategy using the progeny of a residual heterozygous line (RHL) from the RIL was employed to isolate the gene responsible for this quantitative trait locus. A GIGANTEA ortholog, GmGIa (Glyma10g36600), was identified as a candidate gene. A common premature stop codon at the 10th exon was present in the Misuzudaizu allele and in other near isogenic lines (NILs) originating from Harosoy (e2/e2; PI548573). Furthermore, a mutant line harboring another premature stop codon showed an earlier flowering phenotype than the original variety, Bay (E2/E2; PI553043). The e2/e2 genotype exhibited elevated expression of GmFT2a, one of the florigen genes that leads to early flowering. The effects of the E2 allele on flowering time were similar among NILs and constant under high (43°N) and middle (36°N) latitudinal regions in Japan. These results indicate that GmGIa is the gene responsible for the E2 locus and that a null mutation in GmGIa may contribute to the geographic adaptation of soybean.
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Affiliation(s)
- Satoshi Watanabe
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Zhengjun Xia
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150040, People's Republic of China
| | | | - Yasutaka Tsubokura
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan
| | - Naoki Yamanaka
- Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan
| | - Ryoji Takahashi
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan and
| | - Toyoaki Anai
- Faculty of Agriculture, Saga University, Saga 840-8502, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0812, Japan
| | - Keisuke Kitamura
- Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Kyuya Harada
- National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan
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250
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Hu W, Feng B, Ma H. Ectopic expression of the Arabidopsis MINI ZINC FINGER1 and MIF3 genes induces shoot meristems on leaf margins. PLANT MOLECULAR BIOLOGY 2011; 76:57-68. [PMID: 21455630 DOI: 10.1007/s11103-011-9768-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Accepted: 03/10/2011] [Indexed: 05/28/2023]
Abstract
A leaf undergoes determinate growth from a primordium on flank of the shoot apical meristem. Several intrinsic pathways restrict meristematic activity in the leaf of Arabidopsis; however, other factors remain to be defined. We report here that the overexpression of MINI ZINC FINGER1 (MIF1) or MIF3 disrupted the leaf determinate growth by inducing ectopic shoot meristems on leaf margins. These ectopic meristems occurred along margins of late rosette leaves at serration sinuses in an ERECTA-dependent manner. Expression of STM was activated in these ectopic meristems but not other leaf regions. The formation of ectopic meristems was independent of the BP gene but suppressed by exogenous gibberellic acid. In addition, reduced auxin response along leaf margins and subsequent response peak in the sinus were correlated with the occurrence of ectopic meristems. Our results suggest that the sinus of leaf serration is a quiescent domain possessing the potential for meristem formation. MIF1- or MIF3-overexpressing transgenic plants may provide a new genetic system for dissecting the molecular mechanism that maintains leaf determinate growth, and for understanding the interactions between hormone actions and meristematic activity.
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Affiliation(s)
- Wei Hu
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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