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 and He, Zhesi and Wang, Lihong and Langer, Swen and Harper, Andrea L. and Kaur, Harjeevan and Broadley, Martin R. and Gegas, Vasilis and Bancroft, I. (2017) 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 . ISSN 1365-313X

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Abstract

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.

Item Type: Article
Keywords: association genetics, transcriptomics, Brassica napus, tocopherol, erucic acid
Schools/Departments: University of Nottingham, UK > Faculty of Science > School of Biosciences > Division of Plant and Crop Sciences
Identification Number: 10.1111/tpj.13767
Depositing User: Eprints, Support
Date Deposited: 04 Dec 2017 14:00
Last Modified: 05 Dec 2017 10:00
URI: http://eprints.nottingham.ac.uk/id/eprint/48509

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