Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds
An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were score...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
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Wiley
2018
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| Online Access: | https://eprints.nottingham.ac.uk/48509/ |
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| author | Havlickova, Lenka He, Zhesi Wang, Lihong Langer, Swen Harper, Andrea L. Kaur, Harjeevan Broadley, Martin R. Gegas, Vasilis Bancroft, I. |
| author_facet | Havlickova, Lenka He, Zhesi Wang, Lihong Langer, Swen Harper, Andrea L. Kaur, Harjeevan Broadley, Martin R. Gegas, Vasilis Bancroft, I. |
| author_sort | Havlickova, Lenka |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| description | An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high-erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor-effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take-one-out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ-tocopherol methyl transferase converting γ-tocopherol into α-tocopherol) associated with the observed trait variation. The establishment of the first full-scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops. |
| first_indexed | 2025-11-14T20:09:19Z |
| format | Article |
| id | nottingham-48509 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T20:09:19Z |
| publishDate | 2018 |
| publisher | Wiley |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-485092020-05-04T19:53:04Z https://eprints.nottingham.ac.uk/48509/ Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds Havlickova, Lenka He, Zhesi Wang, Lihong Langer, Swen Harper, Andrea L. Kaur, Harjeevan Broadley, Martin R. Gegas, Vasilis Bancroft, I. An updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single-nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high-erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor-effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take-one-out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ-tocopherol methyl transferase converting γ-tocopherol into α-tocopherol) associated with the observed trait variation. The establishment of the first full-scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops. Wiley 2018-01 Article PeerReviewed Havlickova, Lenka, He, Zhesi, Wang, Lihong, Langer, Swen, Harper, Andrea L., Kaur, Harjeevan, Broadley, Martin R., Gegas, Vasilis and Bancroft, I. (2018) Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds. The Plant Journal, 93 (1). pp. 181-192. ISSN 1365-313X association genetics transcriptomics Brassica napus tocopherol erucic acid http://onlinelibrary.wiley.com/doi/10.1111/tpj.13767/abstract doi:10.1111/tpj.13767 doi:10.1111/tpj.13767 |
| spellingShingle | association genetics transcriptomics Brassica napus tocopherol erucic acid Havlickova, Lenka He, Zhesi Wang, Lihong Langer, Swen Harper, Andrea L. Kaur, Harjeevan Broadley, Martin R. Gegas, Vasilis Bancroft, I. Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title | Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title_full | Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title_fullStr | Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title_full_unstemmed | Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title_short | Validation of an updated Associative Transcriptomics platform for the polyploid crop species Brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| title_sort | validation of an updated associative transcriptomics platform for the polyploid crop species brassica napus by dissection of the genetic architecture of erucic acid and tocopherol isoform variation in seeds |
| topic | association genetics transcriptomics Brassica napus tocopherol erucic acid |
| url | https://eprints.nottingham.ac.uk/48509/ https://eprints.nottingham.ac.uk/48509/ https://eprints.nottingham.ac.uk/48509/ |