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Comprehensive analysis of CCCH zinc-finger-type transcription factors in the Brassica rapa genome
Jana Jeevan Rameneni,Vignesh Dhandapani,Parameswari Paul,Sangeeth Prasath Devaraj,최수련,이소영,김만선,홍성민,오상헌,오만호,임용표 한국원예학회 2018 Horticulture, Environment, and Biotechnology Vol.59 No.5
The CCCH-type zinc finger proteins are characterized by their signature motif of three cysteine and one histidine residues. These proteins are RNA binding proteins that function in plant growth, developmental processes, and responses to various environmental stress conditions. In this study, a comprehensive analysis using computational methods allowed the identification of 63 functionally important CCCH genes in the Brassica rapa genome. Several analyses were carried out on the identified genes to understand their roles in this plant. Comparative phylogenetic analysis classified CCCH genes into six clusters, while motif and structural analyses revealed four unique CCCH motifs including different functional motifs and intron/exon variations unique to plants compared to those in other species. Real-time qRT-PCR analysis of 10 randomly selected genes indicated they function at the early stages rather than the later stages of cold and salt stress. This study provides a basic understanding of potential candidate CCCH genes in B. rapa, their structural variation, expression patterns, and their roles under different stress conditions.
Jana Jeevan Rameneni,So Young Yi,Myungjin Lee,Seul Gi Song,Lu Lu,Sang Heon Oh,Song Yeon Han,Yong Pyo Lim 한국원예학회 2021 한국원예학회 학술발표요지 Vol.2021 No.10
Leaf senescence is a developmental process induced by various molecular and environmental stimuli that may affect crop yield. The dark-induced leaf senescence-91 (DLS-91) plants displayed rapid leaf senescence, dramatically decreased chlorophyll contents, low photochemical efficiencies, and upregulation of the senescence-associated marker gene BrSAG12-1. To understand DLS molecular mechanism, we examined transcriptomic changes in DLS-91 and control line DLS-42 following 0, 1, and 4 days of dark treatment (DDT) stages. We identified 501, 446, and 456 DEGs, of which 16.7%, 17.2%, and 14.4% encoded TFs, in samples from the three stages. qRT-PCR validation of 16 genes, namely, 7 MADS, 6 NAC, and 3 WRKY, suggested that BrAGL8-1, BrAGL15-1, and BrWRKY70-1 contribute to the rap id leaf senescence of DLS-91 before (0 DDT) and after (1 and 4 DDT) dark treatment, whereas BrNAC046-2, BrNAC029-2/BrNAP, and BrNAC092-1/ORE1 TFs may regulate this process at a later stage ( 4 DDT). In-silico analysis of cis-acting regulatory elements of BrAGL8-1, BrAGL42-1, BrNAC029-2, BrNAC092-1, and BrWRKY70-3 of B. rapa provides insight into the regulation of these genes. Our study has uncovered several AGL-MADS, WRKY, and NAC TFs potentially worthy of further study to understand the underlying mechanism of rapid DLS in DLS-91.
Jana Jeevan Rameneni,임용표,Vignesh Dhandapani,Parameswari Paul,임수빈,오만호,최수련 한국유전학회 2014 Genes & Genomics Vol.36 No.4
The involvement of MADS-box transcriptionfactors in the development of seeds, flowers, and fruit iswell known. Large numbers of MADS-box genes havebeen characterized and reported in major plants such asArabidopsis thaliana (107), Oryza sativa (75), Zea mays(75), and Cucumis sativus (43). However, there is littleinformation about MADS-box genes in the economicallyand morphologically important genus Brassica. Thus, weperformed a series of computational analyses on therecently published Brassica rapa genome and identified167 potential MADS-box genes. Chromosomal localizationof these genes revealed many duplicate genes and 10 tandemrepeats from B. rapa chromosomes, though none onA04, A08, and A10. Neighbor-joining phylogenetic analysiswas performed between B. rapa, A. thaliana, O. sativa,Z. mays, and C. sativus genes, and type-I and type-IIgroups were differentiated by their gene clades. Based ontheir phylogeny and functional characters, type-I group wasdivided into three clades and type-II group into 14 clades. Prediction and comparison of intron and exon patterns ofMADS-box genes authenticates the major differencebetween the groups. Semi-quantitative RT-PCR analysiswas carried out for 25 functionally categorized BrMADSboxgenes and comparatively studied among buds, sepals,petals, stamens, carpels, and siliques of the parental lineRcBr. The structural and functional annotation, as well asexpressional profiling of BrMADS in floral organs in thisstudy will be the basis of further functional validation andmolecular breeding of B. rapa crops.
Identification of glucosinolate-associated QTLs in cabbage (Brassica oleracea L. var. capitata)
오상헌,최수련,Wenxing Pang,Jana Jeevan Rameneni,이소영,김만선,임수빈,임용표 충남대학교 농업과학연구소 2018 Korean Journal of Agricultural Science Vol.45 No.1
Glucosinolates are one of the important plant secondary metabolites that are produced mainly in Brassicaceae plants. The compounds are primarily involved in defense responses to biotic and abiotic resistance in plants and play important biological roles during plant growth and development. In this study, the glucosinolate profiles in leaves of two different Brassica oleracea populations were compared using high-performance liquid chromatography (HPLC). The nine major glucosinolates compounds in cabbage leaves were identified as belonging to the aliphatic and indolic groups. Among them, sinigrin, which belongs to the aliphatic group, was recorded to be 41% whereas glucobrassicin and 4-methoxyglucobrassicin, which belong to the indolic group, were recorded to be 53.8%. In addition, we performed a genetic analysis to identify regions of the genome regulating glucosinolates biosynthesis in the F3 population of Brassica oleracea. A total of 9 glucosinolates were used for the quantitative trait locus (QTL) analysis. Out of 9, a total of 3 QTLs were identified and they were associated with sinigrin, glucobrassicin, and 4-methoxyglucobrassicin synthesis located in Chromosome 1 and Chromosome 8, respectively. The results of this study will provide valuable information for the breeding of cabbage containing high glucosinolate content, and our next target is to develop component-specific and tightly linked markers for various glucosinolates.
Myungjin Lee,So Young Yi,Jana Jeevan Rameneni,Lu Lu,Chetan Kaur,Yong Pyo Lim 한국원예학회 2021 한국원예학회 학술발표요지 Vol.2021 No.10
Nitrogen (N) deficiency is a main environmental factor that induces early senescence. Cotyledons provide an important N source during germination and early seedling development. In this study, we observed that N deficient condition enhanced gene expression involved in purine catabolism in cotyledons of Chinese cabbage (Brassica rapa ssp. Pekinensis). Seedlings grown with added allopurinol, an inhibitor of xanthine dehydrogenase, in the growth medium showed reduced chlorophyll degradation in cotyledons and lower fresh weight, compared with seedlings grown on normal medium. On the basis of these results, we speculated that xanthine-derived metabolites might affect both seedling growth and early senescence in cotyledons. To confirm this, seedlings were grown with exogenous xanthine to analyze the role of xanthine-derived metabolites under N deficient condition. Seedlings with xanthine as the sole N-source grew faster, and more cotyledon chlorophyll was broken down, compared with seedlings grown without xanthine. The expression levels of senescence- and purine metabolism-related genes in cotyledons were higher than those in seedlings grown without xanthine. These results indicate the possibility that xanthine plays a role as an activator in both purine catabolism and chlorophyll degradation in cotyledons under N deficient condition.