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Nugroho ABD, Kim S, Lee SW, Kim DH. Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa. FRONTIERS IN PLANT SCIENCE 2023; 14:1079218. [PMID: 36890886 PMCID: PMC9986605 DOI: 10.3389/fpls.2023.1079218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Polycomb group proteins (PcG) play a crucial role in developmental programs in eukaryotic organisms, including plants. PcG-mediated gene repression is achieved by epigenetic histone modification on target chromatins. Loss of PcG components leads to severe developmental defects. CURLY LEAF (CLF), a PcG component in Arabidopsis, catalyzes the trimethylation of histone H3 on lysine 27 (H3K27me3), a repressive histone mark in numerous genes in Arabidopsis. In this study, we isolated a single homolog of Arabidopsis CLF, namely, BrCLF, in Brassica rapa ssp. trilocularis. Transcriptomic analysis revealed that BrCLF participated in B. rapa developmental processes, such as seed dormancy, leaf and flower organ development, and floral transition. BrCLF was also involved in stress signaling and stress-responsive metabolism, such as aliphatic and indolic glucosinolate metabolism in B. rapa. Epigenome analysis showed that H3K27me3 was substantially enriched in genes related to these developmental and stress-responsive processes. Thus, this study provided a basis for elucidating the molecular mechanism of the PcG-mediated regulation of development and stress responses in B. rapa.
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Kim JA, Moon H, Kim HS, Choi D, Kim NS, Jang J, Lee SW, Baskoro Dwi Nugroho A, Kim DH. Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants. FRONTIERS IN PLANT SCIENCE 2023; 13:1067508. [PMID: 36743533 PMCID: PMC9891538 DOI: 10.3389/fpls.2022.1067508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Glucosinolates (GSLs) are secondary metabolites providing defense against pathogens and herbivores in plants, and anti-carcinogenic activity against human cancer cells. Profiles of GSLs vary greatly among members of genus Brassica. In this study, we found that a reference line of Chinese cabbage (B. rapa ssp. pekinensis), 'Chiifu' contains significantly lower amounts of total GSLs than the oilseed-type B. rapa (B. rapa ssp. trilocularis) line 'LP08'. This study aimed to identify the key regulators of the high accumulation of GSLs in Brassica rapa plants using transcriptomic and linkage mapping approaches. Comparative transcriptome analysis showed that, in total, 8,276 and 9,878 genes were differentially expressed between 'Chiifu' and 'LP08' under light and dark conditions, respectively. Among 162 B. rapa GSL pathway genes, 79 were related to GSL metabolism under light conditions. We also performed QTL analysis using a single nucleotide polymorphism-based linkage map constructed using 151 F5 individuals derived from a cross between the 'Chiifu' and 'LP08' inbred lines. Two major QTL peaks were successfully identified on chromosome 3 using high-performance liquid chromatography to obtain GSL profiles from 97 F5 recombinant inbred lines. The MYB-domain transcription factor gene BrMYB28.1 (Bra012961) was found in the highest QTL peak region. The second highest peak was located near the 2-oxoacid-dependent dioxygenase gene BrGSL-OH.1 (Bra022920). This study identified major genes responsible for differing profiles of GSLs between 'Chiifu' and 'LP08'. Thus, our study provides molecular insights into differences in GSL profiles between vegetative- and oilseed-type B. rapa plants.
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Affiliation(s)
- Jin A. Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea
| | - Heewon Moon
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Hyang Suk Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea
| | - Dasom Choi
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | - Nan-Sun Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea
| | - Juna Jang
- Department of Agricultural Biotechnology, National Institute of Agricultural Science, Rural Development Administration, Jeonju, Jeollabuk-do, Republic of Korea
| | - Sang Woo Lee
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
| | | | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, Republic of Korea
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Wei Q, Hu T, Xu X, Tian Z, Bao C, Wang J, Pang H, Hu H, Yan Y, Liu T, Wang W. The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa. Genes (Basel) 2022; 13:genes13071162. [PMID: 35885945 PMCID: PMC9317459 DOI: 10.3390/genes13071162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 12/10/2022] Open
Abstract
Flowering time is an important agronomic trait in Brassica rapa and has a wide range of variation. The change from vegetative to reproductive development is a major transition period, especially in flowering vegetable crops. In this study, two non-heading Chinese cabbage varieties with significantly different flowering times, Pak-choi (B. rapa var. communis Tesn et Lee) and Caitai (B. rapa var. tsaitai Hort.), were used to construct segregated F2 populations. The bulk-segregant approach coupled with whole genome re-sequencing was used for QTL sequencing (QTL-seq) analysis to map flowering time traits. The candidate genes controlling flowering time in B. rapa were predicted by homologous gene alignment and function annotation. The major-effect QTL ft7.1 was detected on chromosome A07 of B. rapa, and the FT family gene BrFT was predicted as the candidate gene. Moreover, a new promoter regional difference of 1577 bp was revealed by analyzing the sequence of the BrFT gene. The promoter region activity analysis and divergent gene expression levels indicated that the difference in the promoter region may contribute to different flowering times. These findings provide insights into the mechanisms underlying the flowering time in Brassica and the candidate genes regulating flowering in production.
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Affiliation(s)
- Qingzhen Wei
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Tianhua Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Xinfeng Xu
- Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing 210095, China;
| | - Zhen Tian
- College of Ecology, Lishui University, Lishui 323000, China;
| | - Chonglai Bao
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Jinglei Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Hongtao Pang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Haijiao Hu
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Yaqin Yan
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
| | - Tongkun Liu
- Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing 210095, China;
- Correspondence: (T.L.); (W.W.); Tel.: +86-571-86409722 (W.W.)
| | - Wuhong Wang
- Institute of Vegetables Research, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Q.W.); (T.H.); (C.B.); (J.W.); (H.P.); (H.H.); (Y.Y.)
- Correspondence: (T.L.); (W.W.); Tel.: +86-571-86409722 (W.W.)
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