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Kim G, Cho H, Kim S. Identification of a candidate gene for the I locus determining the dominant white bulb color in onion (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:118. [PMID: 38709404 DOI: 10.1007/s00122-024-04626-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 04/14/2024] [Indexed: 05/07/2024]
Abstract
KEY MESSAGE Through a map-based cloning approach, a gene coding for an R2R3-MYB transcription factor was identified as a causal gene for the I locus controlling the dominant white bulb color in onion. White bulb colors in onion (Allium cepa L.) are determined by either the C or I loci. The causal gene for the C locus was previously isolated, but the gene responsible for the I locus has not been identified yet. To identify candidate genes for the I locus, an approximately 7-Mb genomic DNA region harboring the I locus was obtained from onion and bunching onion (A. fistulosum) whole genome sequences using two tightly linked molecular markers. Within this interval, the AcMYB1 gene, known as a positive regulator of anthocyanin production, was identified. No polymorphic sequences were found between white and red AcMYB1 alleles in the 4,860-bp full-length genomic DNA sequences. However, a 4,838-bp LTR-retrotransposon was identified in the white allele, in the 79-bp upstream coding region from the stop codon. The insertion of this LTR-retrotransposon created a premature stop codon, resulting in the replacement of 26 amino acids with seven different residues. A molecular marker was developed based on the insertion of this LTR-retrotransposon to genotype the I locus. A perfect linkage between bulb color phenotypes and marker genotypes was observed among 5,303 individuals of segregating populations. The transcription of AcMYB1 appeared to be normal in both red and white onions, but the transcription of CHS-A, which encodes chalcone synthase and is involved in the first step of the anthocyanin biosynthesis pathway, was inactivated in the white onions. Taken together, an aberrant AcMYB1 protein produced from the mutant allele might be responsible for the dominant white bulb color in onions.
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Affiliation(s)
- Geonjoong Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea
| | - Heejung Cho
- Genomics Division, National Institute of Agricultural Sciences, RDA, Jeonju, 54874, Republic of Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 61186, Republic of Korea.
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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Jo C, Kim S. Transposition of a non-autonomous DNA transposon in the gene coding for a bHLH transcription factor results in a white bulb color of onions (Allium cepa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:317-328. [PMID: 31637460 DOI: 10.1007/s00122-019-03460-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
A DNA transposon was found in the gene encoding a bHLH transcription factor. Genotypes of the marker tagging this DNA transposon perfectly co-segregated with color phenotypes in large F2:3 populations A combined approach of bulked segregant analysis and RNA-Seq was used to isolate causal gene for C locus controlling white bulb color in onions (Allium cepa L.). A total of 114 contigs containing homozygous single nucleotide polymorphisms (SNPs) between white and yellow bulked RNAs were identified. Four of them showed high homologies with loci clustered in the middle of chromosome 5. SNPs in 34 contigs were confirmed by sequencing of PCR products. One of these contigs showed perfect linkage to the C locus in F2:3 populations consisting of 2491 individuals. However, genotypes of molecular marker tagging this contig were inconsistent with color phenotypes of diverse breeding lines. A total of 146 contigs showed differential expression between yellow and white bulks. Among them, transcription levels of B2 gene encoding a bHLH transcription factor were significantly reduced in white RNA bulk and F2:3 individuals, although there was no SNP in the coding region. Phylogenetic analysis showed that onion B2 was orthologous to bHLH-coding genes regulating anthocyanin biosynthesis pathway in other plant species. Promoter regions of B2 gene were obtained by genome walking and a 577-bp non-autonomous DNA transposon designated as AcWHITE was found in the white allele. Molecular marker tagging AcWHITE showed perfect linkage with the C locus. Marker genotypes of the white allele were detected in some white accessions. However, none of tested red or yellow onions contained AcWHITE insertion, implying that B2 gene was likely to be a casual gene for the C locus.
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Affiliation(s)
- Changyeong Jo
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Korea
| | - Sunggil Kim
- Department of Horticulture, Biotechnology Research Institute, Chonnam National University, Gwangju, 500-757, Korea.
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Holappa LD, Ronald PC, Kramer EM. Evolutionary Analysis of Snf1-Related Protein Kinase2 (SnRK2) and Calcium Sensor (SCS) Gene Lineages, and Dimerization of Rice Homologs, Suggest Deep Biochemical Conservation across Angiosperms. FRONTIERS IN PLANT SCIENCE 2017; 8:395. [PMID: 28424709 PMCID: PMC5381359 DOI: 10.3389/fpls.2017.00395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 03/08/2017] [Indexed: 05/14/2023]
Abstract
Members of the sucrose non-fermenting related kinase Group2 (SnRK2) subclasses are implicated in both direct and indirect abscisic acid (ABA) response pathways. We have used phylogenetic, biochemical, and transient in vivo approaches to examine interactions between Triticum tauschii protein kinase 1 (TtPK1) and an interacting protein, Oryza sativa SnRK2-calcium sensor (OsSCS1). Given that TtPK1 has 100% identity with its rice ortholog, osmotic stress/ABA-activated protein kinase (OsSAPK2), we hypothesized that the SCS and TtPK1 interactions are present in both wheat and rice. Here, we show that SnRK2s are clearly divided into four pan-angiosperm clades with those in the traditionally defined Subclass II encompassing two distinct clades (OsSAPK1/2 and OsSAPK3), although OsSAPK3 lacks an Arabidopsis ortholog. We also show that SCSs are distinct from a second lineage, that we term SCSsister, and while both clades pre-date land plants, the SCSsister clade lacks Poales representatives. Our Y2H assays revealed that the removal of the OsSCS1 C-terminal region along with its N-terminal EF-hand abolished its interaction with the kinase. Using transient in planta bimolecular fluorescence complementation experiments, we demonstrate that TtPK1/OsSCS1 dimerization co-localizes with DAPI-stained nuclei and with FM4-64-stained membranes. Finally, OsSCS1- and OsSAPK2-hybridizing transcripts co-accumulate in shoots/coleoptile of drying seedlings, consistent with up-regulated kinase transcripts of PKABA1 and TtPK1. Our studies suggest that interactions between homologs of the SnRK2 and SCS lineages are broadly conserved across angiosperms and offer new directions for investigations of related proteins.
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Affiliation(s)
- Lynn D. Holappa
- Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA
- Plant Pathology and the Genome Center, University of California DavisDavis, CA, USA
- *Correspondence: Lynn D. Holappa
| | - Pamela C. Ronald
- Plant Pathology and the Genome Center, University of California DavisDavis, CA, USA
| | - Elena M. Kramer
- Organismic and Evolutionary Biology, Harvard UniversityCambridge, MA, USA
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Hooper CM, Castleden IR, Aryamanesh N, Jacoby RP, Millar AH. Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL). PLANT & CELL PHYSIOLOGY 2016; 57:e9. [PMID: 26556651 DOI: 10.1093/pcp/pcv170] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 10/27/2015] [Indexed: 05/10/2023]
Abstract
Barley, wheat, rice and maize provide the bulk of human nutrition and have extensive industrial use as agricultural products. The genomes of these crops each contains >40,000 genes encoding proteins; however, the major genome databases for these species lack annotation information of protein subcellular location for >80% of these gene products. We address this gap, by constructing the compendium of crop protein subcellular locations called crop Proteins with Annotated Locations (cropPAL). Subcellular location is most commonly determined by fluorescent protein tagging of live cells or mass spectrometry detection in subcellular purifications, but can also be predicted from amino acid sequence or protein expression patterns. The cropPAL database collates 556 published studies, from >300 research institutes in >30 countries that have been previously published, as well as compiling eight pre-computed subcellular predictions for all Hordeum vulgare, Triticum aestivum, Oryza sativa and Zea mays protein sequences. The data collection including metadata for proteins and published studies can be accessed through a search portal http://crop-PAL.org. The subcellular localization information housed in cropPAL helps to depict plant cells as compartmentalized protein networks that can be investigated for improving crop yield and quality, and developing new biotechnological solutions to agricultural challenges.
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Affiliation(s)
- Cornelia M Hooper
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Ian R Castleden
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Nader Aryamanesh
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009, Australia
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Baxevanis AD, Bateman A. The Importance of Biological Databases in Biological Discovery. ACTA ACUST UNITED AC 2015; 50:1.1.1-1.1.8. [PMID: 26094768 DOI: 10.1002/0471250953.bi0101s50] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Biological databases play a central role in bioinformatics. They offer scientists the opportunity to access a wide variety of biologically relevant data, including the genomic sequences of an increasingly broad range of organisms. This unit provides a brief overview of major sequence databases and portals, such as GenBank, the UCSC Genome Browser, and Ensembl. Model organism databases, including WormBase, The Arabidopsis Information Resource (TAIR), and those made available through the Mouse Genome Informatics (MGI) resource, are also covered. Non-sequence-centric databases, such as Online Mendelian Inheritance in Man (OMIM), the Protein Data Bank (PDB), MetaCyc, and the Kyoto Encyclopedia of Genes and Genomes (KEGG), are also discussed.
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Affiliation(s)
| | - Alex Bateman
- European Bioinformatics Institute (EMBL-EBI), Hinxton, United Kingdom
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Yim WC, Yu Y, Song K, Jang CS, Lee BM. PLANEX: the plant co-expression database. BMC PLANT BIOLOGY 2013; 13:83. [PMID: 23688397 PMCID: PMC3663717 DOI: 10.1186/1471-2229-13-83] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/16/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND The PLAnt co-EXpression database (PLANEX) is a new internet-based database for plant gene analysis. PLANEX (http://planex.plantbioinformatics.org) contains publicly available GeneChip data obtained from the Gene Expression Omnibus (GEO) of the National Center for Biotechnology Information (NCBI). PLANEX is a genome-wide co-expression database, which allows for the functional identification of genes from a wide variety of experimental designs. It can be used for the characterization of genes for functional identification and analysis of a gene's dependency among other genes. Gene co-expression databases have been developed for other species, but gene co-expression information for plants is currently limited. DESCRIPTION We constructed PLANEX as a list of co-expressed genes and functional annotations for Arabidopsis thaliana, Glycine max, Hordeum vulgare, Oryza sativa, Solanum lycopersicum, Triticum aestivum, Vitis vinifera and Zea mays. PLANEX reports Pearson's correlation coefficients (PCCs; r-values) that distribute from a gene of interest for a given microarray platform set corresponding to a particular organism. To support PCCs, PLANEX performs an enrichment test of Gene Ontology terms and Cohen's Kappa value to compare functional similarity for all genes in the co-expression database. PLANEX draws a cluster network with co-expressed genes, which is estimated using the k-mean method. To construct PLANEX, a variety of datasets were interpreted by the IBM supercomputer Advanced Interactive eXecutive (AIX) in a supercomputing center. CONCLUSION PLANEX provides a correlation database, a cluster network and an interpretation of enrichment test results for eight plant species. A typical co-expressed gene generates lists of co-expression data that contain hundreds of genes of interest for enrichment analysis. Also, co-expressed genes can be identified and cataloged in terms of comparative genomics by using the 'Co-expression gene compare' feature. This type of analysis will help interpret experimental data and determine whether there is a common term among genes of interest.
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Affiliation(s)
- Won Cheol Yim
- Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul, 100-715, Korea
| | - Yongbin Yu
- Department of Healthcare informatics, The Catholic University of Korea, Seoul, 137-701, Korea
| | - Kitae Song
- Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul, 100-715, Korea
| | - Cheol Seong Jang
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon, 200-701, Korea
| | - Byung-Moo Lee
- Department of Plant Biotechnology, Dongguk Univ-Seoul, Seoul, 100-715, Korea
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Cannon EKS, Birkett SM, Braun BL, Kodavali S, Jennewein DM, Yilmaz A, Antonescu V, Antonescu C, Harper LC, Gardiner JM, Schaeffer ML, Campbell DA, Andorf CM, Andorf D, Lisch D, Koch KE, McCarty DR, Quackenbush J, Grotewold E, Lushbough CM, Sen TZ, Lawrence CJ. POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2011; 2011:923035. [PMID: 22253616 PMCID: PMC3255282 DOI: 10.1155/2011/923035] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Accepted: 11/29/2011] [Indexed: 05/21/2023]
Abstract
The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time-sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn's utility are provided herein.
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Affiliation(s)
- Ethalinda K. S. Cannon
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Scott M. Birkett
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Bremen L. Braun
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Sateesh Kodavali
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Douglas M. Jennewein
- Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA
| | - Alper Yilmaz
- Plant Biotechnology Center and Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Valentin Antonescu
- Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Sm822, Boston, MA 02215, USA
| | - Corina Antonescu
- Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Sm822, Boston, MA 02215, USA
| | - Lisa C. Harper
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
- USDA-ARS Plant Gene Expression Center, Albany, CA 94710, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jack M. Gardiner
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA
| | - Mary L. Schaeffer
- USDA-ARS Plant Genetics Research Unit, University of Missouri, Columbia, MO 65211, USA
- Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO 65211, USA
| | - Darwin A. Campbell
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carson M. Andorf
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Destri Andorf
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
| | - Damon Lisch
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Karen E. Koch
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Donald R. McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - John Quackenbush
- Department of Biostatistics and Computational Biology and Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Sm822, Boston, MA 02215, USA
| | - Erich Grotewold
- Plant Biotechnology Center and Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Carol M. Lushbough
- Department of Computer Science, University of South Dakota, Vermillion, SD 57069, USA
| | - Taner Z. Sen
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
| | - Carolyn J. Lawrence
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA
- USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA 50011, USA
- *Carolyn J. Lawrence:
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