A premature stop codon in BrFLC2 transcript results in early flowering in oilseed-type Brassica rapa plants

Kim, Sujeong; Kim, Jin A.; Kang, Hyung Koo; Kim, Dong-Hwan

doi:10.1007/s11103-021-01231-y

Cited by 4 publications

(7 citation statements)

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“…Previously, we developed a mapping population comprised of F 5 151 RILs through the crossing of ‘Chiifu’ and ‘LP08’ ( Kim et al., 2022 ). Among the 151 F 5 RILs, the seeds of 97 germinated successfully and grew well.…”

Section: Resultsmentioning

confidence: 99%

“…trilocularis) ‘LP08’ line were used in this study. For the mapping population, 151 individuals in the F5 generation of a Brassica rapa segregating population were obtained by crossing the ‘Chiifu’ and ‘LP08’ lines in the greenhouse of Rural Development Administration of Korea as described previously ( Kim et al., 2017 ; Kim et al., 2022 ). This population was used for QTL mapping of GSL contents.…”

Section: Methodsmentioning

confidence: 99%

“…All 151 F 5 lines, as well as the two parental lines, were subjected to GBS using the Illumina NextSeq500 sequencing platform, as described previously ( Kim et al., 2022 ). GBS libraries were sequenced on the NextSeq500 system (Illumina, USA) and single-end reads 150 bp in length were obtained.…”

Section: Methodsmentioning

confidence: 99%

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Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants

Kim

Moon²,

Kim³

et al. 2023

Front. Plant Sci.

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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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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants

Kim

Moon²,

Kim³

et al. 2023

Front. Plant Sci.

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“…Several QTL mapping studies have been reported on flowering time in B. rapa and have identified QTL regions where the FLC genes were predicted as candidate genes [ 44 , 49 , 50 ]. In oilseed-type B. rapa , QTL mapping and transcriptome analysis using ‘Chiifu’ and ‘LP08′ as parental materials indicated that BrFLC2 is a candidate gene for rapid flowering in the early flowering cultivar ‘LP08′ [ 51 ]. A major QTL on chromosome A02 was detected in several B. rapa populations with BrFLC2 as the candidate gene across different locations and seasons [ 52 ].…”

Section: Discussionmentioning

confidence: 99%

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa

Wei

Xu³

et al. 2022

Genes

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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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“…Purified RNAs were used to synthesize the complementary DNA synthesis using EasyScript RTase (TransGen Biotech, China). Quantitative RT-qPCR (qRT-PCR) reactions were performed using Sol™ 2X Real-Time PCR Smart mix under the following cycling conditions: 95°C for 10 mins followed by 45 cycles of 95°C for 20s, 60°C for 25 s, and 72°C for 35 s. BrPP2Aa (Bra012474) was used as the reference gene ( Kim et al., 2022 ). qRT-PCR reactions were performed with three technical replicates by using the LineGene 9600 Plus (FQD-96A) Real-Time PCR Detection System (BioER, China).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa

Nugroho

Kim²,

Lee³

et al. 2023

Front. Plant Sci.

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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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A premature stop codon in BrFLC2 transcript results in early flowering in oilseed-type Brassica rapa plants

Abstract: Author contributionsS.K., J.A.K., and H.K. derived the RILs and performed the molecular experiments; S.K., J.A.K., and D.H.K. planned the experiments and analyzed the data; S.K. and D.H.K performed transcriptome analysis; D.H.K. supervised and completed the writing.

Cited by 4 publications

References 55 publications

Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants

Transcriptome and QTL mapping analyses of major QTL genes controlling glucosinolate contents in vegetable- and oilseed-type Brassica rapa plants

The New Variation in the Promoter Region of FLOWERING LOCUS T Is Involved in Flowering in Brassica rapa

Transcriptomic and epigenomic analyses revealed that polycomb repressive complex 2 regulates not only developmental but also stress responsive metabolism in Brassica rapa

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