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
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 famil...
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BMC
2018-05-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-4795-6 |
| _version_ | 1811220706278506496 |
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| author | Steve Babben Edgar Schliephake Philipp Janitza Thomas Berner Jens Keilwagen Michael Koch Fernando Alberto Arana-Ceballos Sven Eduard Templer Yuriy Chesnokov Tatyana Pshenichnikova Jörg Schondelmaier Andreas Börner Klaus Pillen Frank Ordon Dragan Perovic |
| author_facet | Steve Babben Edgar Schliephake Philipp Janitza Thomas Berner Jens Keilwagen Michael Koch Fernando Alberto Arana-Ceballos Sven Eduard Templer Yuriy Chesnokov Tatyana Pshenichnikova Jörg Schondelmaier Andreas Börner Klaus Pillen Frank Ordon Dragan Perovic |
| author_sort | Steve Babben |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T07:47:26Z |
| format | Article |
| id | doaj.art-2557f94932a945298ea5fcb5895882ae |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-12T07:47:26Z |
| publishDate | 2018-05-01 |
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| series | BMC Genomics |
| spelling | doaj.art-2557f94932a945298ea5fcb5895882ae2022-12-22T03:41:41ZengBMCBMC Genomics1471-21642018-05-0119112410.1186/s12864-018-4795-6Association 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 genesSteve Babben0Edgar Schliephake1Philipp Janitza2Thomas Berner3Jens Keilwagen4Michael Koch5Fernando Alberto Arana-Ceballos6Sven Eduard Templer7Yuriy Chesnokov8Tatyana Pshenichnikova9Jörg Schondelmaier10Andreas Börner11Klaus Pillen12Frank Ordon13Dragan Perovic14Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceMartin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional SciencesJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant BiotechnologyJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant BiotechnologyDeutsche Saatveredelung AG (DSV)Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and ReproductionJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceAgrophysical Research Institute (AFI)Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of SciencesSaaten-Union Biotec GmbHLeibniz Institute of Plant Genetics and Crop Plant Research (IPK), Resources Genetics and ReproductionMartin Luther University Halle-Wittenberg (MLU), Institute of Agricultural and Nutritional SciencesJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceJulius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress ToleranceAbstract 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.http://link.springer.com/article/10.1186/s12864-018-4795-6Triticum aestivum L.Frost tolerance (FT)Candidate genesAssociation studiesSNPIndel |
| spellingShingle | Steve Babben Edgar Schliephake Philipp Janitza Thomas Berner Jens Keilwagen Michael Koch Fernando Alberto Arana-Ceballos Sven Eduard Templer Yuriy Chesnokov Tatyana Pshenichnikova Jörg Schondelmaier Andreas Börner Klaus Pillen Frank Ordon Dragan Perovic 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 Triticum aestivum L. Frost tolerance (FT) Candidate genes Association studies SNP Indel |
| title | 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 |
| title_full | 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 |
| title_fullStr | 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 |
| title_full_unstemmed | 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 |
| title_short | 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 |
| title_sort | 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 |
| topic | Triticum aestivum L. Frost tolerance (FT) Candidate genes Association studies SNP Indel |
| url | http://link.springer.com/article/10.1186/s12864-018-4795-6 |
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