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 Common metabolic networks contribute to carbon sink strength of sorghum internodes: implications for bioenergy improvement

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Yin Li ◽  
Min Tu ◽  
Yaping Feng ◽  
Wenqin Wang ◽  
Joachim Messing
Keyword(s):  
Candidate Genes ◽  
Sweet Sorghum ◽  
Metabolic Networks ◽  
Carbon Allocation ◽  
Carbon Sink ◽  
Sink Strength ◽  
Primary Metabolism ◽  
Data Sets ◽  
Rna Seq ◽  
The Common

Abstract Background Sorghum bicolor (L.) is an important bioenergy source. The stems of sweet sorghum function as carbon sinks and accumulate large amounts of sugars and lignocellulosic biomass and considerable amounts of starch, therefore providing a model of carbon allocation and accumulation for other bioenergy crops. While omics data sets for sugar accumulation have been reported in different genotypes, the common features of primary metabolism in sweet genotypes remain unclear. To obtain a cohesive and comparative picture of carbohydrate metabolism between sorghum genotypes, we compared the phenotypes and transcriptome dynamics of sugar-accumulating internodes among three different sweet genotypes (Della, Rio, and SIL-05) and two non-sweet genotypes (BTx406 and R9188). Results Field experiments showed that Della and Rio had similar dynamics and internode patterns of sugar concentration, albeit distinct other phenotypes. Interestingly, cellulose synthases for primary cell wall and key genes in starch synthesis and degradation were coordinately upregulated in sweet genotypes. Sweet sorghums maintained active monolignol biosynthesis compared to the non-sweet genotypes. Comparative RNA-seq results support the role of candidate Tonoplast Sugar Transporter gene (TST), but not the Sugars Will Eventually be Exported Transporter genes (SWEETs) in the different sugar accumulations between sweet and non-sweet genotypes. Conclusions Comparisons of the expression dynamics of carbon metabolic genes across the RNA-seq data sets identify several candidate genes with contrasting expression patterns between sweet and non-sweet sorghum lines, including genes required for cellulose and monolignol synthesis (CesA, PTAL, and CCR), starch metabolism (AGPase, SS, SBE, and G6P-translocator SbGPT2), and sucrose metabolism and transport (TPP and TST2). The common transcriptome features of primary metabolism identified here suggest the metabolic networks contributing to carbon sink strength in sorghum internodes, prioritize the candidate genes for manipulating carbon allocation with bioenergy purposes, and provide a comparative and cohesive picture of the complexity of carbon sink strength in sorghum stem.

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

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 Leafy head formation of the progenies of transgenic plants of Chinese cabbage with exogenous auxin genes

Cell Research ◽  
2000 ◽  
Vol 10 (2) ◽  
pp. 151-160 ◽  
Author(s):  
Yu Ke HE ◽  
Wan Xin XUE ◽  
Yu Dong SUN ◽  
Xu Hong YU ◽  
Ping Lin LIU
Keyword(s):  
Transgenic Plants ◽  
Chinese Cabbage ◽  
Exogenous Auxin ◽  
Head Formation ◽  
Leafy Head

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

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
XiaoXue Sun ◽  
Ram Kumar Basnet ◽  
Zhichun Yan ◽  
Johan Bucher ◽  
Chengcheng Cai ◽  
...  
Keyword(s):  
Developmental Stage ◽  
Chinese Cabbage ◽  
Transcriptome Analysis ◽  
Transcript Abundance ◽  
Specific Gene ◽  
Molecular Pathways ◽  
Pak Choi ◽  
Genome Wide ◽  
Head Formation ◽  
Leafy Head

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.

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.

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