BrRNE cleaves RNA in chloroplasts, regulating retrograde signals in Brassica rapa L. ssp. pekinensis

Abstract Key message Brassica rapa RNE participates in the processing of polycistronic precursor transcripts into mature monocistronic mRNAs in plastids, thereby sending strong retrograde signals. Abstract Leaf color is one of the most important agronomic traits for Chinese cabbage. Not only is it closely linked to photosynthesis, thereby affecting plant growth, but it also influences consumer preference in the marketplace. A pale-green mutant rne was produced by EMS mutagenesis of Chinese cabbage inbred line A03. Chlorophyll content, photosynthetic rate, actual quantum efficiency (φPSII), and maximum quantum efficiency (Fv/Fm) of photosystem II (PSII) were all reduced in rne plants. Genetic analysis indicated that the pale-green trait was controlled by a pair of recessive alleles. Using mixed pool sequencing of F2 individuals derived from an rne × wild-type cross, we identified the essential gene Brassica rapa RNase E (BrRNE), which is responsible for chloroplast development. BrRNE cleaves polycistronic RNA in Chinese cabbage A03 plastids, but rne plants are defective in RNA processing and show reduced translation levels of the seven plastid genes, BrpsaB, BrpsaA, BrpsbA, BrpsbD, BrpsbB, BrpetA, and Brycf4. Abnormal RNA processing in the plastids sends retrograde signals that markedly regulate the expression of nuclear genes, upregulating genes that participate in ribosome and DNA replication pathways and repressing photosynthesis-associated nuclear genes (PhANGs). Our study reveals a new regulatory mechanism by which plastid RNA cleavage influences plastid development and leaf color, sending retrograde signals that affect the expression of nuclear genes in Brassica.

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Identification of two recessive etiolation genes (py1, py2) in pakchoi (Brassica rapa L. ssp. chinensis)

10.21203/rs.2.15677/v4 ◽

2020 ◽

Author(s):

Kun Zhang ◽

Yu Mu ◽

Weijia Li ◽

Xiaofei Shan ◽

Nan Wang ◽

...

Keyword(s):

Brassica Rapa ◽

Molecular Mechanisms ◽

Crop Yields ◽

Microspore Culture ◽

Differentially Expressed Gene ◽

Nuclear Genes ◽

Single Amino Acid ◽

Leaf Color ◽

Chlorophyll Metabolism ◽

Metabolism Regulation

Abstract Background: Leaf color is a major agronomic trait, which has a strong influence on crop yields. Isolating leaf color mutants can represent valuable materials for research in chlorophyll biosynthesis and metabolism regulation. Results: In this study, we identified a stably inherited yellow leaf mutant derived from ‘Huaguan’ pakchoi variety via isolated microspore culture and designated as pylm. This mutant displayed yellow leaves after germination. Its etiolated phenotype was nonlethal and stable during the whole growth period. Its growth was weak and its hypocotyls were markedly elongated. Genetic analysis revealed that two recessive nuclear genes, named py1 and py2, are responsible for the etiolation phenotype. Bulked segregant RNA sequencing (BSR-Seq) showed that py1 and py2 were mapped on chromosomes A09 and A07, respectively. The genes were single Mendelian factors in F3:4 populations based on a 3:1 phenotypic segregation ratio. The py1 was localized to a 258.3-kb interval on a 34-gene genome. The differentially expressed gene BraA09004189 was detected in the py1 mapping region and regulated heme catabolism. One single-nucleotide polymorphism (SNP) of BraA09004189 occurred in pylm. A candidate gene-specific SNP marker in 1,520 F3:4 yellow-colored individuals co-segregated with py1. For py2, 1,860 recessive homozygous F3:4 individuals were investigated and localized py2 to a 4.4-kb interval. Of the five genes in this region, BraA07001774 was predicted as a candidate for py2. It encoded an embryo defective 1187 and a phosphotransferase related to chlorophyll deficiency and hypocotyl elongation. One SNP of BraA07001774 occurred in pylm. It caused a single amino acid mutation from Asp to Asn. According to quantitative real-time polymerase chain reaction (qRT-PCR), BraA07001774 was downregulated in pylm. Conclusions: Our study identified a Chl deficiency mutant pylm in pakchoi. Two recessive nuclear genes named py1 and py2 had a significant effect on etiolation. Candidate genes regulating etiolation were identified as BraA09004189 and BraA07001774, respectively. These findings will elucidate chlorophyll metabolism and the molecular mechanisms of the gene interactions controlling pakchoi etiolation. Keywords: Brassica rapa,·BSR-Seq,·etiolation mutant,·genetic mapping

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Ogura-CMS in Chinese cabbage (Brassica rapa ssp. pekinensis) causes delayed expression of many nuclear genes

Plant Science ◽

10.1016/j.plantsci.2012.11.001 ◽

2013 ◽

Vol 199-200 ◽

pp. 7-17 ◽

Cited By ~ 17

Author(s):

Xiangshu Dong ◽

Wan Kyu Kim ◽

Yong-Pyo Lim ◽

Yeon-Ki Kim ◽

Yoonkang Hur

Keyword(s):

Brassica Rapa ◽

Chinese Cabbage ◽

Nuclear Genes

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Comprehensive Analysis of the Histone Deacetylase Gene Family in Chinese Cabbage (Brassica rapa): From Evolution and Expression Pattern to Functional Analysis of BraHDA3

Agriculture ◽

10.3390/agriculture11030244 ◽

2021 ◽

Vol 11 (3) ◽

pp. 244

Author(s):

Seung Hee Eom ◽

Tae Kyung Hyun

Keyword(s):

Functional Analysis ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Stress Responses ◽

Histone Deacetylases ◽

Expression Patterns ◽

Evolutionary Relationship ◽

Gene Families ◽

Physiological Processes ◽

Lysine Residues

Histone deacetylases (HDACs) are known as erasers that remove acetyl groups from lysine residues in histones. Although plant HDACs play essential roles in physiological processes, including various stress responses, our knowledge concerning HDAC gene families and their evolutionary relationship remains limited. In Brassica rapa genome, we identified 20 HDAC genes, which are divided into three major groups: RPD3/HDA1, HD2, and SIR2 families. In addition, seven pairs of segmental duplicated paralogs and one pair of tandem duplicated paralogs were identified in the B. rapa HDAC (BraHDAC) family, indicating that segmental duplication is predominant for the expansion of the BraHDAC genes. The expression patterns of paralogous gene pairs suggest a divergence in the function of BraHDACs under various stress conditions. Furthermore, we suggested that BraHDA3 (homologous of Arabidopsis HDA14) encodes the functional HDAC enzyme, which can be inhibited by Class I/II HDAC inhibitor SAHA. As a first step toward understanding the epigenetic responses to environmental stresses in Chinese cabbage, our results provide a solid foundation for functional analysis of the BraHDAC family.

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Insights into mechanisms involved in the uptake, translocation, and metabolism of phthalate esters in Chinese cabbage (Brassica rapa var. chinensis)

The Science of The Total Environment ◽

10.1016/j.scitotenv.2021.144945 ◽

2021 ◽

Vol 768 ◽

pp. 144945

Author(s):

Zhipeng Cheng ◽

Yu Wang ◽

Biting Qiao ◽

Qiuyue Zhang ◽

Hongwen Sun

Keyword(s):

Brassica Rapa ◽

Chinese Cabbage ◽

Phthalate Esters

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Metabolomic analysis reveals the interaction of primary and secondary metabolism in white, pale green, and green pak choi (Brassica rapa subsp. chinensis)

Applied Biological Chemistry ◽

10.1186/s13765-020-00574-2 ◽

2021 ◽

Vol 64 (1) ◽

Author(s):

Hyeon Ji Yeo ◽

Seung-A Baek ◽

Ramaraj Sathasivam ◽

Jae Kwang Kim ◽

Sang Un Park

Keyword(s):

Secondary Metabolites ◽

Brassica Rapa ◽

High Performance ◽

Reducing Power ◽

Total Phenolic ◽

Pak Choi ◽

Primary And Secondary Metabolites ◽

Chlorophyll Contents ◽

Significant Difference ◽

Pale Green

AbstractThis study aimed to comprehensively analyze primary and secondary metabolites of three different-colored (white, pale green, and green) pak choi cultivars (Brassica rapa subsp. chinensis) using gas chromatography attached with time-of-flight mass spectrometry (GC-TOFMS) and high-performance liquid chromatography (HPLC). In total, 53 primary metabolites were identified and subjected to partial least-squares discriminant analysis. The result revealed a significant difference in the primary and secondary metabolites between the three pak choi cultivars. In addition, 49 hydrophilic metabolites were detected in different cultivars. Total phenolic and glucosinolate contents were highest in the pale green and green cultivars, respectively, whereas total carotenoid and chlorophyll contents were highest in the white cultivar. Superoxide dismutase activity, 2,2-diphenyl-1-picrylhydraz scavenging, and reducing power were slightly increased in the white, pale green, and green cultivars, respectively. In addition, a negative correlation between pigments and phenylpropanoids was discovered by metabolite correlation analysis. This approach will provide useful information for the development of strategies to enhance the biosynthesis of phenolics, glucosinolates, carotenoids, and chlorophyll, and to improve antioxidant activity in pak choi cultivars. In addition, this study supports the use of HPLC and GC-TOFMS-based metabolite profiling to explore differences in pak choi cultivars.

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