Transcription Coactivator ANGUSTIFOLIA3 (AN3) Regulates Leafy Head Formation in Chinese Cabbage

AbstractChinese 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.

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Conjunctive Analyses of BSA-Seq and BSR-Seq to Reveal the Molecular Pathway of Leafy Head Formation in Chinese Cabbage

Plants ◽

10.3390/plants8120603 ◽

2019 ◽

Vol 8 (12) ◽

pp. 603

Author(s):

Rui Li ◽

Zhongle Hou ◽

Liwei Gao ◽

Dong Xiao ◽

Xilin Hou ◽

...

Keyword(s):

Candidate Genes ◽

Chinese Cabbage ◽

Bulked Segregant Analysis ◽

Rna Seq ◽

Kinase Gene ◽

Head Development ◽

Head Formation ◽

The Common ◽

Leafy Head ◽

Candidate Regions

As the storage organ of Chinese cabbage, the leafy head was harvested as a commercial product due to its edible value. In this study, the bulked segregant analysis (BSA) and bulked segregant RNA-Seq (BSR) were performed with F2 separation progeny to study the molecular mechanism of leafy head formation in Chinese cabbage. BSA-Seq analysis located four candidate regions containing 40 candidate genes, while BSR-Seq analysis revealed eight candidate regions containing 607 candidate genes. The conjunctive analyses of these two methods identified that Casein kinase gene BrCKL8 (Bra035974) is the common candidate gene related with leafy head formation in Chinese cabbage, and it showed high expression levels at the three segments of heading type plant leaves. The differentially expressed genes (DEGs) between two set pairs of cDNA sequencing bulks were divided into two categories: one category was related with five hormone pathways (Auxin, Ethylene, Abscisic acid, Jasmonic acid and Gibberellin), the other category was composed of genes that associate with the calcium signaling pathway. Moreover, a series of upregulated transcriptional factors (TFs) were also identified by the association analysis of BSR-Seq analysis. The leafy head development was regulated by various biological processes and effected by diverse external environment factors, so our research will contribute to the breeding of perfect leaf-heading types of Chinese cabbage.

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Series-Spatial Transcriptome Profiling of Leafy Head Reveals the Key Transition Leaves for Head Formation in Chinese Cabbage

Frontiers in Plant Science ◽

10.3389/fpls.2021.787826 ◽

2022 ◽

Vol 12 ◽

Author(s):

Xinlei Guo ◽

Jianli Liang ◽

Runmao Lin ◽

Lupeng Zhang ◽

Jian Wu ◽

...

Keyword(s):

Genetic Control ◽

Chinese Cabbage ◽

Morphological Differentiation ◽

Sugar Metabolism ◽

Transcriptome Profiling ◽

Complex Signal ◽

Head Formation ◽

Leaf Tissues ◽

Leafy Head ◽

Heading Stage

Chinese cabbage is an important leaf heading vegetable crop. At the heading stage, its leaves across inner to outer show significant morphological differentiation. However, the genetic control of this complex leaf morphological differentiation remains unclear. Here, we reported the transcriptome profiling of Chinese cabbage plant at the heading stage using 24 spatially dissected tissues representing different regions of the inner to outer leaves. Genome-wide transcriptome analysis clearly separated the inner leaf tissues from the outer leaf tissues. In particular, we identified the key transition leaf by the spatial expression analysis of key genes for leaf development and sugar metabolism. We observed that the key transition leaves were the first inwardly curved ones. Surprisingly, most of the heading candidate genes identified by domestication selection analysis obviously showed a corresponding expression transition, supporting that key transition leaves are related to leafy head formation. The key transition leaves were controlled by a complex signal network, including not only internal hormones and protein kinases but also external light and other stimuli. Our findings provide new insights and the rich resource to unravel the genetic control of heading traits.

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Morphological and genetic characterization of the leafy head of Chinese cabbage (Brassica rapa)

10.18174/457901 ◽

2018 ◽

Author(s):

Xiao Xue Sun

Keyword(s):

Brassica Rapa ◽

Chinese Cabbage ◽

Genetic Characterization ◽

Leafy Head

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Transcriptome profiling of yellow leafy head development during the heading stage in Chinese cabbage (Brassica rapasubsp.pekinensis)

Physiologia Plantarum ◽

10.1111/ppl.12784 ◽

2018 ◽

Vol 165 (4) ◽

pp. 800-813 ◽

Cited By ~ 2

Author(s):

Yuefei Li ◽

Yong Fan ◽

Yang Jiao ◽

Jie Wu ◽

Zhen Zhang ◽

...

Keyword(s):

Chinese Cabbage ◽

Transcriptome Profiling ◽

Head Development ◽

Leafy Head ◽

Heading Stage

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Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa

Genome Biology ◽

10.1186/s13059-021-02383-2 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xu Cai ◽

Lichun Chang ◽

Tingting Zhang ◽

Haixu Chen ◽

Lei Zhang ◽

...

Keyword(s):

Brassica Rapa ◽

Structural Variation ◽

De Novo ◽

Individual Genome ◽

Synonymous Mutations ◽

Pan Genome ◽

Intact Gene ◽

Head Formation ◽

Leafy Head

Abstract Background Despite the prevalence and recurrence of polyploidization in the speciation of flowering plants, its impacts on crop intraspecific genome diversification are largely unknown. Brassica rapa is a mesopolyploid species that is domesticated into many subspecies with distinctive morphotypes. Results Herein, we report the consequences of the whole-genome triplication (WGT) on intraspecific diversification using a pan-genome analysis of 16 de novo assembled and two reported genomes. Among the genes that derive from WGT, 13.42% of polyploidy-derived genes accumulate more transposable elements and non-synonymous mutations than other genes during individual genome evolution. We denote such genes as being “flexible.” We construct the Brassica rapa ancestral genome and observe the continuing influence of the dominant subgenome on intraspecific diversification in B. rapa. The gene flexibility is biased to the more fractionated subgenomes (MFs), in contrast to the more intact gene content of the dominant LF (least fractionated) subgenome. Furthermore, polyploidy-derived flexible syntenic genes are implicated in the response to stimulus and the phytohormone auxin; this may reflect adaptation to the environment. Using an integrated graph-based genome, we investigate the structural variation (SV) landscapes in 524 B. rapa genomes. We observe that SVs track morphotype domestication. Four out of 266 candidate genes for Chinese cabbage domestication are speculated to be involved in the leafy head formation. Conclusions This pan-genome uncovers the possible contributions of allopolyploidization on intraspecific diversification and the possible and underexplored role of SVs in favorable trait domestication. Collectively, our work serves as a rich resource for genome-based B. rapa improvement.

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