Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response

Shannon Woodhouse,Rachel Wells,Richard J Morris,Ian Bancroft,Judith A Irwin,Zhesi He,Hugh Woolfenden,Wilfried Haerty,Burkhard Steuernagel

doi:10.1186/s12864-021-07805-w

Shannon Woodhouse, Rachel Wells + Show 7 more

Open Access

https://doi.org/10.1186/s12864-021-07805-w

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Abstract

BackgroundAssociative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood.ResultsHere, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response.ConclusionsThis study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.

Highlights

Ensuring synchronous transiting from the vegetative to the reproductive phase is important for maximising the harvestable produce from brassica vegetables
Using our validated population structure with associative mapping, we identified candidates orthologous to Genome-wide association studies (GWAS) analysis identified a significant association with BoFLC.C2 and the difference in days to buds visible’ (DTB) and days to first flower’ (DTF) following a ten-week pre-growth period, with six weeks of vernalisation at 5 oC
Identifying genes underlying phenotypic traits in B. oleracea is an important step for the improvement of brassica vegetables

Summary

Introduction

Ensuring synchronous transiting from the vegetative to the reproductive phase is important for maximising the harvestable produce from brassica vegetables. B. oleracea L., is a cruciferous perennial growing naturally along the coastlines of Western Europe. From this single species, selective breeding efforts have enabled the production of the numerous subspecies we see today. The shift from the vegetative to reproductive phase is important and being able to genetically manipulate this transition will aid the development and production of synchronous brassica vegetables. Within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood

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