Biology subjects

Woolfenden, H.

Publications and source records attributed to Woolfenden, H..

3 recordsLinked to original sources

bioRxiv2026

Transcriptome profiling reveals gene regulatory network governing seed size in Brassica napus

Seed size is a critical trait influencing yield and quality in oilseed crops such as Brassica napus. Despite their economic importance, the genetic and molecular mechanisms regulating seed size remain unclear, particularly in polyploid species, such as B. napus. To deepen our understanding of seed size regulation, we performed a comprehensive transcriptomic analysis across four developmental stages (heart, torpedo, green, and mature) and three distinct seed organs: the seed coat, embryo, and endosperm. Differential expression analysis between B. napus var. Zhongshuang (ZS11) and B. napus cv. Ragged Jack (RJ) was performed to uncover regulatory networks involved in seed size control. Our results uncovered dynamic gene regulatory networks (GRNs) and pinpointed key regulators, including well-established factors like ABI5 and BRI1, as well as novel candidate genes such as KNAT5, ARF11, SUS2, UGT72B1, UGT89A2, and SBT1.7. The present research provides an understanding of the regulatory networks governing seed size in B. napus. These findings not only enhance our knowledge of seed biology but also offer valuable resources for future breeding strategies aimed at optimizing seed size and yield in polyploid oilseed crops.

genomics↗

bioRxiv2025

Network analysis of flowering time genes suggests regulatory changes among SOC1 orthologues in response to cold in Brassica napus

Flowering plants respond to multiple environmental and endogenous cues to determine the timing of their transition from the vegetative to floral state. Most of our knowledge of the gene regulatory network (GRN) controlling flowering time has been derived from the model plant Arabidopsis thaliana. This knowledge needs to be translated to crop plants to support the development of varieties that can be grown in different and rapidly changing climatic conditions. However, due to increased genome complexity and limited prior knowledge, translation into crops is not always straightforward. Here, we present a study of the GRN controlling flowering time in Brassica napus (oilseed rape), an allotetraploid crop that is a close relative of Arabidopsis. Using a comparative transcriptomics approach, we show that the majority of the orthologous gene pairs have similar expression dynamics over development between Arabidopsis and Brassica napus. Some genes, however, have experienced regulatory changes, with flowering time genes in Brassica napus having higher than average differences in their expression profiles from their Arabidopsis orthologues. Despite these differences, the inferred GRN for flowering in Brassica napus exhibits a similar network topology to the network known in Arabidopsis. This is likely due to preferential retention of these genes in higher paralogue numbers, which allows subtle changes in the regulation of individual paralogues, while still conserving the overall regulatory structure through evolution. We discover and present a detailed analysis of one such example where orthologues of SUPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) have similar expression patterns under normal conditions, but different dynamics under cold temperature conditions, suggesting possible subfunctionalisation among paralogues in response to temperature change.

plant biology↗

bioRxiv2020

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

Associative 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. Here, 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. This study 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.

plant biology↗