Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)

XiaoXue Sun; Ram Kumar Basnet; Zhichun Yan; Johan Bucher; Chengcheng Cai; Jianjun Zhao; Guusje Bonnema

doi:10.1038/s41438-019-0212-9

Genome-wide transcriptome analysis reveals molecular pathways involved in leafy head formation of Chinese cabbage (Brassica rapa)

Hortic Res. 2019 Dec 1:6:130. doi: 10.1038/s41438-019-0212-9. eCollection 2019.

Authors

XiaoXue Sun^{1

2}, Ram Kumar Basnet³, Zhichun Yan², Johan Bucher², Chengcheng Cai², Jianjun Zhao¹, Guusje Bonnema^{1

2}

Affiliations

¹ 1Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, Department of Horticulture, Hebei Agricultural University, Baoding, 071001 China.
² 2Plant Breeding, Wageningen University and Research, Wageningen, 6708PB The Netherlands.
³ Quantitative genetics department, Rijk Zwaan Breeding B.V., Eerste Kruisweg 9, Fijnaart, 4793 RS The Netherlands.

Abstract

Chinese cabbage plants go through seedling and rosette stages before forming their leafy head. Chinese cabbage plants resemble pak-choi plants at their seedling stage, but in their rosette stage the leaves of Chinese cabbage differentiate, as they increase in size with shorter petioles. In order to understand the molecular pathways that play a role in leafy head formation, transcript abundance of young emerging leaves was profiled during development of two Chinese cabbage genotypes and a single pak-choi genotype. The two Chinese cabbages differed in many aspects, among others earliness, leaf size and shape, leaf numbers, and leafy head shape. Genome-wide transcriptome analysis clearly separated the seedling stages of all three genotypes together with the later stages from pak-choi, from the later developmental stages of both Chinese cabbages (rosette, folding, and heading). Weighted correlation network analysis and hierarchical clustering using Euclidean distances resulted in gene clusters with transcript abundance patterns distinguishing the two Chinese cabbages from pak-choi. Three clusters included genes with transcript abundance affected by both genotype and developmental stage, whereas two clusters showed only genotype effects. This included a genotype by developmental stage cluster highly enriched with the MapMan category photosynthesis, with high expression during rosette and folding in Chinese cabbages and low expression in the heading inner leaves that are not exposed to light. The other clusters contained many genes in the MapMan categories Cell, showing again differences between pak-choi and both Chinese cabbages. We discuss how this relates to the differences in leaf blade growth between Chinese cabbage and pak-choi, especially at the rosette stage. Overall, comparison of the transcriptome between leaves of two very different Chinese cabbages with pak-choi during plant development allowed the identification of specific gene categories associated with leafy head formation.

Keywords: Gene expression; Plant development.