1
|
Coulton A, Edwards KJ. AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids. BMC Bioinformatics 2020; 21:311. [PMID: 32677889 PMCID: PMC7364506 DOI: 10.1186/s12859-020-03601-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 06/11/2020] [Indexed: 12/02/2022] Open
Abstract
Background Polyploid organisms such as wheat complicate even the simplest of procedures in molecular biology. Whilst knowledge of genomic sequences in crops is increasing rapidly, the scientific community is still a long way from producing a full pan-genome for every species. Polymerase chain reaction and Sanger sequencing therefore remain widely used as methods for characterizing gene sequences in many varieties of crops. High sequence similarity between genomes in polyploids means that if primers are not homeologue-specific via the incorporation of a SNP at the 3’ tail, sequences other than the target sequence will also be amplified. Current consensus for gene cloning in wheat is to manually perform many steps in a long bioinformatics pipeline. Results Here we present AutoCloner (www.autocloner.com), a fully automated pipeline for crop gene cloning that includes a free-to-use web interface for users. AutoCloner takes a sequence of interest from the user and performs a basic local alignment search tool (BLAST) search against the genome assembly for their particular polyploid crop. Homologous sequences are then compiled with the input sequence into a multiple sequence alignment which is mined for single-nucleotide polymorphisms (SNPs). Various combinations of potential primers that cover the entire gene of interest are then created and evaluated by Primer3; the set of primers with the highest score, as well as all possible primers at every SNP location, are then returned to the user for polymerase chain reaction (PCR). We have successfully used AutoCloner to clone various genes of interest in the Apogee wheat variety, which has no current genome sequence. In addition, we have successfully run the pipeline on ~ 80,000 high-confidence gene models from a wheat genome assembly. Conclusion AutoCloner is the first tool to fully-automate primer design for gene cloning in polyploids, where previously the consensus within the wheat community was to perform this process manually. The web interface for AutoCloner provides a simple and effective polyploid primer-design method for gene cloning, with no need for researchers to download software or input any other details other than their sequence of interest.
Collapse
Affiliation(s)
- Alexander Coulton
- Biological Sciences Department, The University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK.
| | - Keith J Edwards
- Biological Sciences Department, The University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
| |
Collapse
|
2
|
Babben S, Schliephake E, Janitza P, Berner T, Keilwagen J, Koch M, Arana-Ceballos FA, Templer SE, Chesnokov Y, Pshenichnikova T, Schondelmaier J, Börner A, Pillen K, Ordon F, Perovic D. Association genetics studies on frost tolerance in wheat (Triticum aestivum L.) reveal new highly conserved amino acid substitutions in CBF-A3, CBF-A15, VRN3 and PPD1 genes. BMC Genomics 2018; 19:409. [PMID: 29843596 PMCID: PMC5975666 DOI: 10.1186/s12864-018-4795-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 05/14/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a complex trait regulated by a number of genes and several gene families. Availability of the wheat genomic sequence opens new opportunities for exploring candidate genes diversity for FT. Therefore, the objectives of this study were to identity SNPs and insertion-deletion (indels) in genes known to be involved in frost tolerance and to perform association genetics analysis of respective SNPs and indels on FT. RESULTS Here we report on the sequence analysis of 19 candidate genes for FT in wheat assembled using the Chinese Spring IWGSC RefSeq v1.0. Out of these, the tandem duplicated C-repeat binding factors (CBF), i.e. CBF-A3, CBF-A5, CBF-A10, CBF-A13, CBF-A14, CBF-A15, CBF-A18, the vernalisation response gene VRN-A1, VRN-B3, the photoperiod response genes PPD-B1 and PPD-D1 revealed association to FT in 235 wheat cultivars. Within six genes (CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1) amino acid (AA) substitutions in important protein domains were identified. The amino acid substitution effect in VRN-A1 on FT was confirmed and new AA substitutions in CBF-A3, CBF-A15, VRN-B3, PPD-B1 and PPD-D1 located at highly conserved sites were detected. Since these results rely on phenotypic data obtained at five locations in 2 years, detection of significant associations of FT to AA changes in CBF-A3, CBF-A15, VRN-A1, VRN-B3, PPD-B1 and PPD-D1 may be exploited in marker assisted breeding for frost tolerance in winter wheat. CONCLUSIONS A set of 65 primer pairs for the genes mentioned above from a previous study was BLASTed against the IWGSC RefSeq resulting in the identification of 39 primer combinations covering the full length of 19 genes. This work demonstrates the usefulness of the IWGSC RefSeq in specific primer development for highly conserved gene families in hexaploid wheat and, that a candidate gene association genetics approach based on the sequence data is an efficient tool to identify new alleles of genes important for the response to abiotic stress in wheat.
Collapse
Affiliation(s)
- Steve Babben
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Edgar Schliephake
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Philipp Janitza
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 5, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Thomas Berner
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Jens Keilwagen
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Michael Koch
- Deutsche Saatveredelung AG (DSV), Weißenburger Str. 5, 59557 Lippstadt, Nordrhein-Westfalen Germany
| | - Fernando Alberto Arana-Ceballos
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and Reproduction, Correnstraße 3, 06466 Seeland OT Gatersleben, Saxony-Anhalt Germany
| | - Sven Eduard Templer
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
- Max Planck Institute for Biology of Ageing, Joseph-Stelzmann-Str. 9B, 50931 Cologne, Nordrhein-Westfalen Germany
| | - Yuriy Chesnokov
- Agrophysical Research Institute (AFI), Grazhdanskii prosp. 14, 195220 St. Petersburg, Russia
| | - Tatyana Pshenichnikova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Prospekt Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Jörg Schondelmaier
- Saaten-Union Biotec GmbH, Hovedisser Str. 94, 33818 Leopoldshoehe, Nordrhein-Westfalen Germany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and Reproduction, Correnstraße 3, 06466 Seeland OT Gatersleben, Saxony-Anhalt Germany
| | - Klaus Pillen
- Martin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional Sciences, Betty-Heimann-Str. 3, 06120 Halle (Saale), Saxony-Anhalt Germany
| | - Frank Ordon
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| | - Dragan Perovic
- Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, Erwin-Baur-Str. 27, 06484 Quedlinburg, Saxony-Anhalt Germany
| |
Collapse
|