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

2018 ◽  
Vol 165 (4) ◽  
pp. 800-813 ◽  
Author(s):  
Yuefei Li ◽  
Yong Fan ◽  
Yang Jiao ◽  
Jie Wu ◽  
Zhen Zhang ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Transcriptome Profiling ◽  
Head Development ◽  
Leafy Head ◽  
Heading Stage

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

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.

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

Plants ◽  
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.

scholarly journals The mutation of ent-kaurene synthase, a key enzyme involved in gibberellin biosynthesis, confers a non-heading phenotype to Chinese cabbage (Brassica rapa L. ssp. pekinensis)

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Yue Gao ◽  
Shengnan Huang ◽  
Gaoyang Qu ◽  
Wei Fu ◽  
Meidi Zhang ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Recessive Gene ◽  
Gibberellin Biosynthesis ◽  
Wild Type ◽  
Specific Pcr ◽  
Head Development ◽  
Nucleotide Mutation ◽  
In The Wild ◽  
Leafy Head ◽  
Heading Chinese Cabbage

Abstract The presence of a leafy head is a vital agronomic trait that facilitates the evaluation of the yield and quality of Chinese cabbage. A non-heading mutant (nhm1) was identified in an ethyl methanesulfonate mutagenesis population of the heading Chinese cabbage double haploid line FT. Segregation analysis revealed that a single recessive gene, Brnhm1, controlled the mutant phenotype. Using MutMap, Kompetitive allele-specific PCR, and cloning analyses, we demonstrated that BraA07g042410.3C, which encodes an ent-kaurene synthase involved in the gibberellin biosynthesis pathway, is the nhm1 mutant candidate gene. A single-nucleotide mutation (C to T) in the fourth exon of BraA07g042410.3C caused an amino acid substitution from histidine to tyrosine. Compared to that of the wild-type FT, BraA07g042410.3C in the leaves of the nhm1 mutant had lower levels of expression. In addition, gibberellin contents were lower in the mutant than in the wild type, and the mutant plant phenotype could be restored to that of the wild type after exogenous GA3 treatment. These results indicate that BraA07g042410.3C caused the non-heading mutation. This is the first study to demonstrate a relationship between gibberellin content in the leaves and leafy head formation in Chinese cabbage. These findings facilitate the understanding of the mechanisms underlying leafy head development in Chinese cabbage.

scholarly journals Dynamic Changes of the Anthocyanin Biosynthesis Mechanism During the Development of Heading Chinese Cabbage (Brassica rapa L.) and Arabidopsis Under the Control of BrMYB2

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiong He ◽  
Qianqian Lu ◽  
Yuting He ◽  
Yaxiu Wang ◽  
Ninan Zhang ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Anthocyanin Biosynthesis ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Anthocyanin Accumulation ◽  
Total Anthocyanin ◽  
Head Development ◽  
Whole Plant ◽  
Heading Chinese Cabbage ◽  
Upregulated Genes

Chinese cabbage is an important vegetable mainly planted in Asian countries, and mining the molecular mechanism responsible for purple coloration in Brassica crops is fast becoming a research hotspot. In particular, the anthocyanin accumulation characteristic of purple heading Chinese cabbage, along with the plant’s growth and head developing, is still largely unknown. To elucidate the dynamic anthocyanin biosynthesis mechanism of Chinese cabbage during its development processes, here we investigated the expression profiles of 86 anthocyanin biosynthesis genes and corresponding anthocyanin accumulation characteristics of plants as they grew and their heads developed, between purple heading Chinese cabbage 11S91 and its breeding parents. Anthocyanin accumulation of 11S91 increased from the early head formation period onward, whereas the purple trait donor 95T2-5 constantly accumulated anthocyanin throughout its whole plant development. Increasing expression levels of BrMYB2 and BrTT8 together with the downregulation of BrMYBL2.1, BrMYBL2.2, and BrLBD39.1 occurred in both 11S91 and 95T2-5 plants during their growth, accompanied by the significantly continuous upregulation of a phenylpropanoid metabolic gene, BrPAL3.1; a series of early biosynthesis genes, such as BrCHSs, BrCHIs, BrF3Hs, and BrF3’H; as well as some key late biosynthesis genes, such as BrDFR1, BrANS1, BrUF3GT2, BrUF5GT, Br5MAT, and Brp-Cout; in addition to the transport genes BrGST1 and BrGST2. Dynamic expression profiles of these upregulated genes correlated well with the total anthocyanin contents during the processes of plant growth and leaf head development, and results supported by similar evidence for structural genes were also found in the BrMYB2 transgenic Arabidopsis. After intersubspecific hybridization breeding, the purple interior heading leaves of 11S91 inherited the partial purple phenotypes from 95T2-5 while the phenotypes of seedlings and heads were mainly acquired from white 94S17; comparatively in expression patterns of investigated anthocyanin biosynthesis genes, cotyledons of 11S91 might inherit the majority of genetic information from the white type parent, whereas the growth seedlings and developing heading tissues of 11S91 featured expression patterns of these genes more similar to 95T2-5. This comprehensive set of results provides new evidence for a better understanding of the anthocyanin biosynthesis mechanism and future breeding of new purple Brassica vegetables.

Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing

2011 ◽  
Vol 30 (1) ◽  
pp. 17-28 ◽  
Author(s):  
Shuancang Yu ◽  
Fenglan Zhang ◽  
Yangjun Yu ◽  
Deshuang Zhang ◽  
Xiuyun Zhao ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Transcriptome Profiling ◽  
Dehydration Stress

EST analysis of the heading leaf of Chinese cabbage (Brassica rapa L. ssp. pekinensis) in the early phase of the heading stage

2004 ◽  
Vol 1 (2) ◽  
pp. 119-124 ◽  
Author(s):  
Gao Rui-Juan ◽  
Dai Da-Peng ◽  
Ma Rong-Cai ◽  
Cao Ming-Qing ◽  
Yan Yue-Ming ◽  
...  
Keyword(s):  
Brassica Rapa ◽  
Chinese Cabbage ◽  
Early Phase ◽  
Developmental Process ◽  
Base Pairs ◽  
Significant Similarity ◽  
Sequencing Project ◽  
Est Analysis ◽  
Heading Stage

AbstractA cDNA library was constructed from the heading leaf in the early phase of the heading stage of Chinese cabbage (Brassica rapa L. ssp. pekinensis). By sequencing the randomly selected clones, 1363 sequences longer than 200 bp were found, with better trace data. After removing the poly(A) and contamination sequences, 1162 ESTs longer than 150 bp were obtained, of which 1102 shared significant similarity with known sequences in protein and nucleotide databases of the National Center for Biotechnology Information (NCBI) as revealed by searches using the BLASTX and BLASTN engines. Functional assignment of the ESTs was based on the method used in the Arabidopsis thaliana genome-sequencing project. About 77% of the putative protein sequences with known biological functions best matched with those of A. thaliana deposited in the non-redundant database of NCBI. These data suggest that Chinese cabbage is closely related to A. thaliana. This result is different from that reported in other Brassica species. At nucleotide level, however, 51% of the ESTs were homologous to those deposited for A. thaliana when all ESTs were searched against the est-others database. In addition, 60 ESTs had no homology with any of the plant gene sequences deposited in GenBank. These ESTs are very important for understanding the unique developmental process of Chinesecabbage and elaborating its genetic mapping. Among the genes with assigned functions, the most abundant representatives were those involved in protein synthesis and energy metabolism. With the 1162 ESTs, 895 non-redundant contigs were generated after being aligned using the Seqman II module of DNAStar software at the threshold of more than 80% homology over a minimum of 40 base pairs. Of these, 723 were singletons containing only one EST sequence, indicating that many kinds of such genes are expressed in the heading leaf of Chinese cabbage. An expression profile of Chinese cabbage heading leaf with the 1162 ESTs was therefore acquired in this work. This could be very useful for uncovering the mechanism of the heading process, which is the most obvious characteristic of Chinese cabbage and perhaps other related species, such as Brassica oleracea. This work could accelerate the finding and characterization of genes specifically expressed in the heading stage of Chinese cabbage.

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

2019 ◽  
Vol 10 ◽  
Author(s):  
Jing Yu ◽  
Liwei Gao ◽  
Wusheng Liu ◽  
Lixiao Song ◽  
Dong Xiao ◽  
...  
Keyword(s):  
Chinese Cabbage ◽  
Head Formation ◽  
Leafy Head ◽  
Transcription Coactivator

scholarly journals Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce

2020 ◽  
Vol 117 (52) ◽  
pp. 33668-33678
Author(s):  
Changchun Yu ◽  
Chenghuan Yan ◽  
Yuling Liu ◽  
Yali Liu ◽  
Yue Jia ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Vegetable Crops ◽  
Mobility Shift ◽  
Unique Type ◽  
Chip Sequencing ◽  
Head Development ◽  
Enhanced Expression ◽  
Trait Locus ◽  
Leafy Head ◽  
Electrophoretic Mobility Shift Assays

Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays. Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.

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