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Havlickova L, He Z, Berger M, Wang L, Sandmann G, Chew YP, Yoshikawa GV, Lu G, Hu Q, Banga SS, Beaudoin F, Bancroft I. Genomics of predictive radiation mutagenesis in oilseed rape: modifying seed oil composition. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:738-750. [PMID: 37921406 PMCID: PMC10893948 DOI: 10.1111/pbi.14220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 10/12/2023] [Accepted: 10/20/2023] [Indexed: 11/04/2023]
Abstract
Rapeseed is a crop of global importance but there is a need to broaden the genetic diversity available to address breeding objectives. Radiation mutagenesis, supported by genomics, has the potential to supersede genome editing for both gene knockout and copy number increase, but detailed knowledge of the molecular outcomes of radiation treatment is lacking. To address this, we produced a genome re-sequenced panel of 1133 M2 generation rapeseed plants and analysed large-scale deletions, single nucleotide variants and small insertion-deletion variants affecting gene open reading frames. We show that high radiation doses (2000 Gy) are tolerated, gamma radiation and fast neutron radiation have similar impacts and that segments deleted from the genomes of some plants are inherited as additional copies by their siblings, enabling gene dosage decrease. Of relevance for species with larger genomes, we showed that these large-scale impacts can also be detected using transcriptome re-sequencing. To test the utility of the approach for predictive alteration of oil fatty acid composition, we produced lines with both decreased and increased copy numbers of Bna.FAE1 and confirmed the anticipated impacts on erucic acid content. We detected and tested a 21-base deletion expected to abolish function of Bna.FAD2.A5, for which we confirmed the predicted reduction in seed oil polyunsaturated fatty acid content. Our improved understanding of the molecular effects of radiation mutagenesis will underpin genomics-led approaches to more efficient introduction of novel genetic variation into the breeding of this crop and provides an exemplar for the predictive improvement of other crops.
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Affiliation(s)
| | - Zhesi He
- Department of BiologyUniversity of YorkYorkUK
| | | | - Lihong Wang
- Department of BiologyUniversity of YorkYorkUK
| | | | | | - Guilherme V. Yoshikawa
- Department of BiologyUniversity of YorkYorkUK
- Present address:
School of Agriculture, Food and Wine, Waite Research InstituteUniversity of AdelaideGlen OsmondSAAustralia
| | - Guangyuan Lu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
- College of Biology and Food EngineeringGuangdong University of Petrochemical TechnologyMaomingChina
| | - Qiong Hu
- Department of Rapeseed Genetics and Breeding, Oil Crops Research InstituteCAASWuhanChina
| | - Surinder S. Banga
- Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia
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Jiang L, Li G, Chern M, Jain R, Pham NT, Martin JA, Schackwitz WS, Zhao J, Ruan D, Huang R, Zheng J, Ronald PC. Whole-Genome Sequencing Identifies a Rice Grain Shape Mutant, gs9-1. RICE (NEW YORK, N.Y.) 2019; 12:52. [PMID: 31321562 PMCID: PMC6639446 DOI: 10.1186/s12284-019-0308-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 06/27/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Breeding for genes controlling key agronomic traits is an important goal of rice genetic improvement. To gain insight into genes controlling grain morphology, we screened M3 plants derived from 1,000 whole-genome sequenced (WGS) M2 Kitaake mutants to identify lines with altered grain size. RESULTS In this study, we isolated a mutant, named fast-neutron (FN) 60-4, which exhibits a significant reduction in grain size. We crossed FN60-4 with the parental line Kitaake and analyzed the resulting backcross population. Segregation analysis of 113 lines from the BC2F2 population revealed that the mutant phenotype is controlled by a single semi-dominant locus. Mutant FN60-4 is reduced 20% in plant height and 8.8% in 1000-grain weight compared with Kitaake. FN60-4 also exhibits an 8% reduction in cell number and a 9% reduction in cell length along the vertical axis of the glume. We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains, and revealed that one gene, LOC_Os09g02650, cosegregated with the grain size phenotype in the BC1F2 and BC2F2 populations. This mutant allele was named grain shape 9-1 (gs9-1). gs9-1 carries a 3-bp deletion that affects two amino acids. This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression, cellulose microfibril deposition and gibberellic acid (GA) biosynthesis. The GA biosynthesis-related gene KO2 is down-regulated in gs9-1. The dwarf phenotype of gs9-1 can be rescued by adding exogenous GA3. In contrast to the phenotypes for the other alleles, the gs9-1 is less severe, consistent with the nature of the mutation, which does not disrupt the open reading frame as observed for the other alleles. CONCLUSIONS In this study, we isolated a mutant, which exhibits altered grain shape and identified the mutated gene, gs9-1. Our study reveals that gs9-1 is a semi-dominant gene that carries a two-amino acid mutation. gs9-1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis. These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice.
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Affiliation(s)
- Liangrong Jiang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, 361102 People’s Republic of China
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Guotian Li
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- State Key Laboratory of Agricultural Microbiology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Rashmi Jain
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Nhan T. Pham
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Joel A. Martin
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Wendy S. Schackwitz
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598 USA
| | - Juan Zhao
- State Key Laboratory of Agricultural Microbiology and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Deling Ruan
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Rongyu Huang
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Jingsheng Zheng
- Xiamen Plant Genetics Key Laboratory, School of Life Sciences, Xiamen University, Xiamen, 361102 People’s Republic of China
| | - Pamela C. Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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Terol J, Nueda MJ, Ventimilla D, Tadeo F, Talon M. Transcriptomic analysis of Citrus clementina mandarin fruits maturation reveals a MADS-box transcription factor that might be involved in the regulation of earliness. BMC PLANT BIOLOGY 2019; 19:47. [PMID: 30704398 PMCID: PMC6357379 DOI: 10.1186/s12870-019-1651-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 01/14/2019] [Indexed: 05/20/2023]
Abstract
BACKGROUND Harvest time is a relevant economic trait in citrus, and selection of cultivars with different fruit maturity periods has a remarkable impact in the market share. Generation of early- and late-maturing cultivars is an important target for citrus breeders, therefore, generation of knowledge regarding the genetic mechanisms controlling the ripening process and causing the early and late phenotypes is crucial. In this work we analyze the evolution of the transcriptome during fruit ripening in 3 sport mutations derived from the Fina clementine (Citrus clementina) mandarin: Clemenules (CLE), Arrufatina (ARR) and Hernandina (HER) that differ in their harvesting periods. CLE is considered a mid-season cultivar while ARR and HER are early- and late-ripening mutants, respectively. RESULTS We used RNA-Seq technology to carry out a time course analysis of the transcriptome of the 3 mutations along the ripening period. The results indicated that in these mutants, earliness and lateness during fruit ripening correlated with the advancement or delay in the expression of a set of genes that may be implicated in the maturation process. A detailed analysis of the transcription factors known to be involved in the regulation of fruit ripening identified a member of the MADS box family whose expression was lower in ARR, the early-ripening mutant, and higher in HER, the late-ripening mutant. The pattern of expression of this gene during the maturation period was basically contrary to those of the ethylene biosynthetic genes, SAM and ACC synthases and ACC oxidase. The gene was present in hemizygous dose in the early-ripening mutant. CONCLUSIONS Our analysis provides new clues about the genetic control of fruit ripening in citrus and allowed the identification of a transcription factor that could be involved in the early phenotype.
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Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - M. José Nueda
- Facultad de Ciencias, Universidad de Alicante, Alicante, Spain
| | - Daniel Ventimilla
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - Francisco Tadeo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada, Valencia Spain
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Chen Y, Wang X, Lu S, Wang H, Li S, Chen R. An Array-based Comparative Genomic Hybridization Platform for Efficient Detection of Copy Number Variations in Fast Neutron-induced Medicago truncatula Mutants. J Vis Exp 2017. [PMID: 29155794 DOI: 10.3791/56470] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutants are invaluable genetic resources for gene function studies. To generate mutant collections, three types of mutagens can be utilized, including biological such as T-DNA or transposon, chemical such as ethyl methanesulfonate (EMS), or physical such as ionization radiation. The type of mutation observed varies depending on the mutagen used. For ionization radiation induced mutants, mutations include deletion, duplication, or rearrangement. While T-DNA or transposon-based mutagenesis is limited to species that are susceptible to transformation, chemical or physical mutagenesis can be applied to a broad range of species. However, the characterization of mutations derived from chemical or physical mutagenesis traditionally relies on a map-based cloning approach, which is labor intensive and time consuming. Here, we show that a high-density genome array-based comparative genomic hybridization (aCGH) platform can be applied to efficiently detect and characterize copy number variations (CNVs) in mutants derived from fast neutron bombardment (FNB) mutagenesis in Medicago truncatula, a legume species. Whole genome sequence analysis shows that there are more than 50,000 genes or gene models in M. truncatula. At present, FNB-induced mutants in M. truncatula are derived from more than 150,000 M1 lines, representing invaluable genetic resources for functional studies of genes in the genome. The aCGH platform described here is an efficient tool for characterizing FNB-induced mutants in M. truncatula.
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Affiliation(s)
- Yuhui Chen
- Laboratory of Plant Genetics and Development, Noble Research Institute
| | - Xianfu Wang
- Genetics Laboratory, University of Oklahoma Health Science Center
| | - Shunfei Lu
- Medicine and Health School, Li Shui University
| | - Hongcheng Wang
- Genetics Laboratory, University of Oklahoma Health Science Center
| | - Shibo Li
- Genetics Laboratory, University of Oklahoma Health Science Center
| | - Rujin Chen
- Laboratory of Plant Genetics and Development, Noble Research Institute;
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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7
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Terol J, Ibañez V, Carbonell J, Alonso R, Estornell LH, Licciardello C, Gut IG, Dopazo J, Talon M. Involvement of a citrus meiotic recombination TTC-repeat motif in the formation of gross deletions generated by ionizing radiation and MULE activation. BMC Genomics 2015; 16:69. [PMID: 25758634 PMCID: PMC4334395 DOI: 10.1186/s12864-015-1280-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/26/2015] [Indexed: 02/07/2023] Open
Abstract
Background Transposable-element mediated chromosomal rearrangements require the involvement of two transposons and two double-strand breaks (DSB) located in close proximity. In radiobiology, DSB proximity is also a major factor contributing to rearrangements. However, the whole issue of DSB proximity remains virtually unexplored. Results Based on DNA sequencing analysis we show that the genomes of 2 derived mutations, Arrufatina (sport) and Nero (irradiation), share a similar 2 Mb deletion of chromosome 3. A 7 kb Mutator-like element found in Clemenules was present in Arrufatina in inverted orientation flanking the 5′ end of the deletion. The Arrufatina Mule displayed “dissimilar” 9-bp target site duplications separated by 2 Mb. Fine-scale single nucleotide variant analyses of the deleted fragments identified a TTC-repeat sequence motif located in the center of the deletion responsible of a meiotic crossover detected in the citrus reference genome. Conclusions Taken together, this information is compatible with the proposal that in both mutants, the TTC-repeat motif formed a triplex DNA structure generating a loop that brought in close proximity the originally distinct reactive ends. In Arrufatina, the loop brought the Mule ends nearby the 2 distinct insertion target sites and the inverted insertion of the transposable element between these target sites provoked the release of the in-between fragment. This proposal requires the involvement of a unique transposon and sheds light on the unresolved question of how two distinct sites become located in close proximity. These observations confer a crucial role to the TTC-repeats in fundamental plant processes as meiotic recombination and chromosomal rearrangements. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1280-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Victoria Ibañez
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - José Carbonell
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Roberto Alonso
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Leandro H Estornell
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
| | - Concetta Licciardello
- CRA-ACM, Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Corso Savoia 190, 95024, Acireale, Catania, Italy.
| | - Ivo G Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, 08028, Barcelona, Spain.
| | - Joaquín Dopazo
- Centro de Investigación Principe Felipe (CIPF), Avda, Autopista del Saler, 16-3, 46012, Valencia, Spain.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias (IVIA), Moncada, 46113, Valencia, Spain.
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8
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Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB, Ries L, Dobbels AA, Campbell BW, Young NP, Anderson JE, Grant DM, Orf JH, Naeve SL, Muehlbauer GJ, Vance CP, Stupar RM. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 2014; 198:967-81. [PMID: 25213171 PMCID: PMC4224183 DOI: 10.1534/genetics.114.170340] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/02/2014] [Indexed: 01/14/2023] Open
Abstract
Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.
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Affiliation(s)
- Yung-Tsi Bolon
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jeffrey Roessler
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Pudota B Bhaskar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Landon Ries
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Austin A Dobbels
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Nathan P Young
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - David M Grant
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | - James H Orf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Seth L Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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9
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Bolon YT, Stec AO, Michno JM, Roessler J, Bhaskar PB, Ries L, Dobbels AA, Campbell BW, Young NP, Anderson JE, Grant DM, Orf JH, Naeve SL, Muehlbauer GJ, Vance CP, Stupar RM. Genome resilience and prevalence of segmental duplications following fast neutron irradiation of soybean. Genetics 2014. [PMID: 25213171 DOI: 10.1534/genetics.114.170340/-/dc1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
Fast neutron radiation has been used as a mutagen to develop extensive mutant collections. However, the genome-wide structural consequences of fast neutron radiation are not well understood. Here, we examine the genome-wide structural variants observed among 264 soybean [Glycine max (L.) Merrill] plants sampled from a large fast neutron-mutagenized population. While deletion rates were similar to previous reports, surprisingly high rates of segmental duplication were also found throughout the genome. Duplication coverage extended across entire chromosomes and often prevailed at chromosome ends. High-throughput resequencing analysis of selected mutants resolved specific chromosomal events, including the rearrangement junctions for a large deletion, a tandem duplication, and a translocation. Genetic mapping associated a large deletion on chromosome 10 with a quantitative change in seed composition for one mutant. A tandem duplication event, located on chromosome 17 in a second mutant, was found to cosegregate with a short petiole mutant phenotype, and thus may serve as an example of a morphological change attributable to a DNA copy number gain. Overall, this study provides insight into the resilience of the soybean genome, the patterns of structural variation resulting from fast neutron mutagenesis, and the utility of fast neutron-irradiated mutants as a source of novel genetic losses and gains.
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Affiliation(s)
- Yung-Tsi Bolon
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jeffrey Roessler
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Pudota B Bhaskar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Landon Ries
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Austin A Dobbels
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Nathan P Young
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Justin E Anderson
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - David M Grant
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, Ames, Iowa 50011
| | - James H Orf
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Seth L Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108 Plant Science Research Unit, United States Department of Agriculture-Agricultural Research Service, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Germana MA, Aleza P, Carrera E, Chen C, Chiancone B, Costantino G, Dambier D, Deng X, Federici CT, Froelicher Y, Guo W, Ibáñez V, Juárez J, Kwok K, Luro F, Machado MA, Naranjo MA, Navarro L, Ollitrault P, Ríos G, Roose ML, Talon M, Xu Q, Gmitter FG. Cytological and molecular characterization of three gametoclones of Citrus clementina. BMC PLANT BIOLOGY 2013; 13:129. [PMID: 24020638 PMCID: PMC3847870 DOI: 10.1186/1471-2229-13-129] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 08/24/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND Three gametoclonal plants of Citrus clementina Hort. ex Tan., cv. Nules, designated ESP, FRA, and ITA (derived from three labs in Spain, France, and Italy, respectively), were selected for cytological and molecular characterization in order to elucidate genomic rearrangements provoked by haploidization. The study included comparisons of their ploidy, homozygosity, genome integrity, and gene dosage, using chromosome counting, flow cytometry, SSR marker genotyping, and array-Comparative Genomic Hybridization (array-CGH). RESULTS Chromosome counting and flow cytometry revealed that ESP and FRA were haploid, but ITA was tri-haploid. Homozygous patterns, represented by a single peak (allele), were observed among the three plants at almost all SSR loci distributed across the entire diploid donor genome. Those few loci with extra peaks visualized as output from automated sequencing runs, generally low or ambiguous, might result from amplicons of paralogous members at the locus, non-specific sites, or unexpected recombinant alleles. No new alleles were found, suggesting the genomes remained stable and intact during gametogenesis and regeneration. The integrity of the haploid genome also was supported by array-CGH studies, in which genomic profiles were comparable to the diploid control. CONCLUSIONS The presence of few gene hybridization abnormalities, corroborated by gene dosage measurements, were hypothetically due to the segregation of hemizygous alleles and minor genomic rearrangements occurring during the haploidization procedure. In conclusion, these plants that are valuable genetic and breeding materials contain completely homozygous and essentially intact genomes.
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Affiliation(s)
- Maria Antonietta Germana
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, 11, Palermo 90128, Italy
| | - Pablo Aleza
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | | | - Chunxian Chen
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL, USA
- USDA-ARS, Southeastern Fruit and Tree Nut Research Laboratory, Byron, GA, USA
| | - Benedetta Chiancone
- Università degli Studi di Palermo, Dipartimento di Scienze Agrarie e Forestali, Viale delle Scienze, 11, Palermo 90128, Italy
| | | | - Dominique Dambier
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Xiuxin Deng
- Huazhong Agricultural University, Wuhan, Hubei, China
| | - Claire T Federici
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | - Yann Froelicher
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Wenwu Guo
- Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - José Juárez
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | - Kevin Kwok
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | | | - Marcos A Machado
- Instituto Agronômico de Campinas, Centro APTA Citros Sylvio Moreira, Cordeirópolis, SP, Brazil
| | | | - Luis Navarro
- IVIA, Centro de Proteccion Vegetal y Biotecnologia, Moncada, Valencia, Spain
| | - Patrick Ollitrault
- CIRAD, Département “Systèmes Biologiques” Unité de Recherche ‘Multiplication Végétative’ Montpellier, Paris, France
| | - Gabino Ríos
- IVIA, Centro de Genómica, Moncada, Valencia, Spain
| | - Mikeal L Roose
- University of California, Department of Botany and Plant Sciences, Riverside, CA, USA
| | - Manuel Talon
- IVIA, Centro de Genómica, Moncada, Valencia, Spain
| | - Qiang Xu
- Huazhong Agricultural University, Wuhan, Hubei, China
| | - Fred G Gmitter
- University of Florida, Citrus Research and Education Center, Lake Alfred, FL, USA
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11
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Abstract
Mutagenesis is frequently used to test gene function and to aid in crop improvement. Targeting Induced Local Lesions in Genomes (TILLING) is a reverse genetic strategy first developed to identify induced point mutations in Arabidopsis. This general strategy has since been applied to many plant and animal species. Here, we describe a protocol for high-throughput TILLING in rice. Gene segments are amplified using fluorescently tagged primers, and products are denatured and reannealed to form heteroduplexes between the mutated and wild-type sequences. These heteroduplexes are substrates for cleavage by single-strand-specific nucleases. Following cleavage, products are analyzed on denaturing polyacrylamide gels using the LI-COR DNA analyzer system. Several rice TILLING populations have been described, and a public mutation screening service is now available. The basic methods used for TILLING can be adapted for the discovery and cataloguing of natural nucleotide variation in populations, a strategy known as Ecotilling, which was first used to study genetic diversity among Arabidopsis ecotypes, and has since been applied to crop plants.
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12
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Caruso M, Merelo P, Distefano G, La Malfa S, Lo Piero AR, Tadeo FR, Talon M, Gentile A. Comparative transcriptome analysis of stylar canal cells identifies novel candidate genes implicated in the self-incompatibility response of Citrus clementina. BMC PLANT BIOLOGY 2012; 12:20. [PMID: 22333138 PMCID: PMC3305554 DOI: 10.1186/1471-2229-12-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 02/14/2012] [Indexed: 05/09/2023]
Abstract
BACKGROUND Reproductive biology in citrus is still poorly understood. Although in recent years several efforts have been made to study pollen-pistil interaction and self-incompatibility, little information is available about the molecular mechanisms regulating these processes. Here we report the identification of candidate genes involved in pollen-pistil interaction and self-incompatibility in clementine (Citrus clementina Hort. ex Tan.). These genes have been identified comparing the transcriptomes of laser-microdissected stylar canal cells (SCC) isolated from two genotypes differing for self-incompatibility response ('Comune', a self-incompatible cultivar and 'Monreal', a self- compatible mutation of 'Comune'). RESULTS The transcriptome profiling of SCC indicated that the differential regulation of few specific, mostly uncharacterized transcripts is associated with the breakdown of self-incompatibility in 'Monreal'. Among them, a novel F-box gene showed a drastic up-regulation both in laser microdissected stylar canal cells and in self-pollinated whole styles with stigmas of 'Comune' in concomitance with the arrest of pollen tube growth. Moreover, we identify a non-characterized gene family as closely associated to the self-incompatibility genetic program activated in 'Comune'. Three different aspartic-acid rich (Asp-rich) protein genes, located in tandem in the clementine genome, were over-represented in the transcriptome of 'Comune'. These genes are tightly linked to a DELLA gene, previously found to be up-regulated in the self-incompatible genotype during pollen-pistil interaction. CONCLUSION The highly specific transcriptome survey of the stylar canal cells identified novel genes which have not been previously associated with self-pollen rejection in citrus and in other plant species. Bioinformatic and transcriptional analyses suggested that the mutation leading to self-compatibility in 'Monreal' affected the expression of non-homologous genes located in a restricted genome region. Also, we hypothesize that the Asp-rich protein genes may act as Ca2+ "entrapping" proteins, potentially regulating Ca2+ homeostasis during self-pollen recognition.
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Affiliation(s)
- Marco Caruso
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Paz Merelo
- Institut Valencià d'Investigacions Agràries - Centre de Genómica, Carretera Montcada de l'Horta-Náquera Km. 4,5, 46113 Montcada de l'Horta (València), Spain
| | - Gaetano Distefano
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Stefano La Malfa
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Angela Roberta Lo Piero
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
| | - Francisco R Tadeo
- Institut Valencià d'Investigacions Agràries - Centre de Genómica, Carretera Montcada de l'Horta-Náquera Km. 4,5, 46113 Montcada de l'Horta (València), Spain
| | - Manuel Talon
- Institut Valencià d'Investigacions Agràries - Centre de Genómica, Carretera Montcada de l'Horta-Náquera Km. 4,5, 46113 Montcada de l'Horta (València), Spain
| | - Alessandra Gentile
- Dipartimento di Scienze delle Produzioni Agrarie e Alimentari, Università degli Studi di Catania, Via Valdisavoia 5, 95123 Catania, Italy
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13
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Ríos G, Naranjo MA, Rodrigo MJ, Alós E, Zacarías L, Cercós M, Talón M. Identification of a GCC transcription factor responding to fruit colour change events in citrus through the transcriptomic analyses of two mutants. BMC PLANT BIOLOGY 2010; 10:276. [PMID: 21159189 PMCID: PMC3014968 DOI: 10.1186/1471-2229-10-276] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Accepted: 12/15/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND External ripening in Citrus fruits is morphologically characterized by a colour shift from green to orange due to the degradation of chlorophylls and the accumulation of carotenoid pigments. Although numerous genes coding for enzymes involved in such biochemical pathways have been identified, the molecular control of this process has been scarcely studied. In this work we used the Citrus clementina mutants 39B3 and 39E7, showing delayed colour break, to isolate genes potentially related to the regulation of peel ripening and its physiological or biochemical effects. RESULTS Pigment analyses revealed different profiles of carotenoid and chlorophyll modification in 39B3 and 39E7 mutants. Flavedo from 39B3 fruits showed an overall delay in carotenoid accumulation and chlorophyll degradation, while the flavedo of 39E7 was devoid of the apocarotenoid β-citraurin among other carotenoid alterations. A Citrus microarray containing about 20,000 cDNA fragments was used to identify genes that were differentially expressed during colour change in the flavedo of 39B3 and 39E7 mutants respect to the parental variety. The results highlighted 73 and 90 genes that were respectively up- and down-regulated in both mutants. CcGCC1 gene, coding for a GCC type transcriptional factor, was found to be down-regulated. CcGCC1 expression was strongly induced at the onset of colour change in the flavedo of parental clementine fruit. Moreover, treatment of fruits with gibberellins, a retardant of external ripening, delayed both colour break and CcGCC1 overexpression. CONCLUSIONS In this work, the citrus fruit ripening mutants 39B3 and 39E7 have been characterized at the phenotypic, biochemical and transcriptomic level. A defective synthesis of the apocarotenoid β-citraurin has been proposed to cause the yellowish colour of fully ripe 39E7 flavedo. The analyses of the mutant transcriptomes revealed that colour change during peel ripening was strongly associated with a major mobilization of mineral elements and with other previously known metabolic and photosynthetic changes. The expression of CcGCC1 was associated with peel ripening since CcGCC1 down-regulation correlated with a delay in colour break induced by genetic, developmental and hormonal causes.
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Affiliation(s)
- Gabino Ríos
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Náquera km 4.5, 46113 Moncada (Valencia), Spain
| | - Miguel A Naranjo
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Náquera km 4.5, 46113 Moncada (Valencia), Spain
| | - María-Jesús Rodrigo
- Departamento de Ciencia de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Apartado de Correos 73, 46100 Burjassot (Valencia), Spain
| | - Enriqueta Alós
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Náquera km 4.5, 46113 Moncada (Valencia), Spain
| | - Lorenzo Zacarías
- Departamento de Ciencia de Alimentos, Instituto de Agroquímica y Tecnología de Alimentos (IATA)-CSIC, Apartado de Correos 73, 46100 Burjassot (Valencia), Spain
| | - Manuel Cercós
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Náquera km 4.5, 46113 Moncada (Valencia), Spain
| | - Manuel Talón
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Náquera km 4.5, 46113 Moncada (Valencia), Spain
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14
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Leida C, Terol J, Martí G, Agustí M, Llácer G, Badenes ML, Ríos G. Identification of genes associated with bud dormancy release in Prunus persica by suppression subtractive hybridization. TREE PHYSIOLOGY 2010; 30:655-66. [PMID: 20231169 DOI: 10.1093/treephys/tpq008] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
To better understand the molecular and physiological mechanisms underlying maintenance and release of seasonal bud dormancy in perennial trees, we identified differentially expressed genes during dormancy progression in reproductive buds from peach (Prunus persica [L.] Batsch) by suppression subtractive hybridization (SSH) and microarray hybridization. Four SSH libraries were constructed, which were respectively enriched in cDNA highly expressed in dormant buds (named DR), in dormancy-released buds (RD) and in the cultivars with different chilling requirement, 'Zincal 5' (ZS) and 'Springlady' (SZ), sampled after dormancy release. About 2500 clones picked from the four libraries were loaded on a glass microarray. Hybridization of microarrays with the final products of SSH procedure was performed in order to validate the selected clones that were effectively enriched in their respective sample. Nearly 400 positive clones were sequenced, which corresponded to 101 different unigenes with diverse functional annotation. We obtained DAM4, 5 and 6 genes coding for MADS-box transcription factors previously related to growth cessation and terminal bud formation in the evergrowing mutant of peach. Several other cDNAs are similar to dormancy factors described in other species, and others have been related to bud dormancy for the first time in this study. Quantitative reverse transcription polymerase chain reaction analysis confirmed differential expression of cDNAs coding for a Zn-finger transcription factor, a GRAS-like regulator, a DNA-binding protein and proteins similar to forisome subunits involved in the reversible occlusion of sieve elements in Fabaceae, among others.
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Affiliation(s)
- Carmen Leida
- Instituto Valenciano de Investigaciones Agrarias, E-46113, Moncada, Valencia, Spain
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15
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Gilchrist E, Haughn G. Reverse genetics techniques: engineering loss and gain of gene function in plants. Brief Funct Genomics 2010; 9:103-10. [DOI: 10.1093/bfgp/elp059] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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16
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Beló A, Beatty MK, Hondred D, Fengler KA, Li B, Rafalski A. Allelic genome structural variations in maize detected by array comparative genome hybridization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:355-67. [PMID: 19756477 DOI: 10.1007/s00122-009-1128-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Accepted: 07/28/2009] [Indexed: 05/04/2023]
Abstract
DNA polymorphisms such as insertion/deletions and duplications affecting genome segments larger than 1 kb are known as copy-number variations (CNVs) or structural variations (SVs). They have been recently studied in animals and humans by using array-comparative genome hybridization (aCGH), and have been associated with several human diseases. Their presence and phenotypic effects in plants have not been investigated on a genomic scale, although individual structural variations affecting traits have been described. We used aCGH to investigate the presence of CNVs in maize by comparing the genome of 13 maize inbred lines to B73. Analysis of hybridization signal ratios of 60,472 60-mer oligonucleotide probes between inbreds in relation to their location in the reference genome (B73) allowed us to identify clusters of probes that deviated from the ratio expected for equal copy-numbers. We found CNVs distributed along the maize genome in all chromosome arms. They occur with appreciable frequency in different germplasm subgroups, suggesting ancient origin. Validation of several CNV regions showed both insertion/deletions and copy-number differences. The nature of CNVs detected suggests CNVs might have a considerable impact on plant phenotypes, including disease response and heterosis.
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Affiliation(s)
- André Beló
- DuPont Crop Genetics, Route 141, Henry Clay Road, Wilmington, DE 19803, USA.
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17
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Papdi C, Joseph MP, Salamó IP, Vidal S, Szabados L. Genetic technologies for the identification of plant genes controlling environmental stress responses. FUNCTIONAL PLANT BIOLOGY : FPB 2009; 36:696-720. [PMID: 32688681 DOI: 10.1071/fp09047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Accepted: 06/11/2009] [Indexed: 06/11/2023]
Abstract
Abiotic conditions such as light, temperature, water availability and soil parameters determine plant growth and development. The adaptation of plants to extreme environments or to sudden changes in their growth conditions is controlled by a well balanced, genetically determined signalling system, which is still far from being understood. The identification and characterisation of plant genes which control responses to environmental stresses is an essential step to elucidate the complex regulatory network, which determines stress tolerance. Here, we review the genetic approaches, which have been used with success to identify plant genes which control responses to different abiotic stress factors. We describe strategies and concepts for forward and reverse genetic screens, conventional and insertion mutagenesis, TILLING, gene tagging, promoter trapping, activation mutagenesis and cDNA library transfer. The utility of the various genetic approaches in plant stress research we review is illustrated by several published examples.
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Affiliation(s)
- Csaba Papdi
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Mary Prathiba Joseph
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Imma Pérez Salamó
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
| | - Sabina Vidal
- Facultad de Ciencias, Universidad de la República, Iguá 4225, CP 11400, Montevideo, Uruguay
| | - László Szabados
- Institute of Plant Biology, Biological Research Centre, 6726-Szeged, Temesvári krt. 62, Hungary
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18
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Gimeno J, Gadea J, Forment J, Pérez-Valle J, Santiago J, Martínez-Godoy MA, Yenush L, Bellés JM, Brumós J, Colmenero-Flores JM, Talón M, Serrano R. Shared and novel molecular responses of mandarin to drought. PLANT MOLECULAR BIOLOGY 2009; 70:403-20. [PMID: 19290483 DOI: 10.1007/s11103-009-9481-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2008] [Accepted: 03/06/2009] [Indexed: 05/20/2023]
Abstract
Drought is the most important stress experienced by citrus crops. A citrus cDNA microarray of about 6.000 genes has been utilized to identify transcriptomic responses of mandarin to water stress. As observed in other plant species challenged with drought stress, key genes for lysine catabolism, proline and raffinose synthesis, hydrogen peroxide reduction, vacuolar malate transport, RCI2 proteolipids and defence proteins such as osmotin, dehydrins and heat-shock proteins are induced in mandarin. Also, some aquaporin genes are repressed. The osmolyte raffinose could be detected in stressed roots while the dehydrin COR15 protein only accumulated in stressed leaves but not in roots. Novel drought responses in mandarin include the induction of genes encoding a new miraculin isoform, chloroplast beta-carotene hydroxylase, oleoyl desaturase, ribosomal protein RPS13A and protein kinase CTR1. These results suggest that drought tolerance in citrus may benefit from inhibition of proteolysis, activation of zeaxanthin and linolenoyl synthesis, reinforcement of ribosomal structure and down-regulation of the ethylene response.
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Affiliation(s)
- Jacinta Gimeno
- Instituto De Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-CSIC, Camino de Vera s/n, Valencia, Spain
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19
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Bruce M, Hess A, Bai J, Mauleon R, Diaz MG, Sugiyama N, Bordeos A, Wang GL, Leung H, Leach JE. Detection of genomic deletions in rice using oligonucleotide microarrays. BMC Genomics 2009; 10:129. [PMID: 19320995 PMCID: PMC2666768 DOI: 10.1186/1471-2164-10-129] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 03/25/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The induction of genomic deletions by physical- or chemical- agents is an easy and inexpensive means to generate a genome-saturating collection of mutations. Different mutagens can be selected to ensure a mutant collection with a range of deletion sizes. This would allow identification of mutations in single genes or, alternatively, a deleted group of genes that might collectively govern a trait (e.g., quantitative trait loci, QTL). However, deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify. Here, we present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment. Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions. RESULTS We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip allows rapid localization of deleted regions in rice mutants. Deletions ranged in size from one gene model to approximately 500 kb and were predicted on all 12 rice chromosomes. The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype. Finally, the positions of mutations in 14 mutants were aligned onto the rice pseudomolecules in a user-friendly genome browser to allow for rapid identification of untagged mutations http://irfgc.irri.org/cgi-bin/gbrowse/IR64_deletion_mutants/. CONCLUSION We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice. The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome. This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.
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Affiliation(s)
- Myron Bruce
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO, USA.
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