Genome-wide analysis of spatiotemporal gene expression patterns during floral organ development in Brassica rapa
Flowering is a key agronomic trait that directly influences crop yield and quality and serves as a model system for elucidating the molecular basis that controls successful reproduction, adaptation, and diversification of flowering plants. Adequate knowledge of continuous series of expression data from the floral transition to maturation is lacking in Brassica rapa. To unravel the genome expression associated with the development of early small floral buds (< 2 mm; FB2), early large floral buds (2-4 mm; FB4), stamens (STs) and carpels (CPs), transcriptome profiling was carried out with a Br300K oligo microarray. The results showed that at least 6848 known nonredundant genes (30% of the genes of the Br300K) were differentially expressed during the floral transition from vegetative tissues to maturation. Functional annotation of the differentially expressed genes (DEGs) (fold change ≥ 5) by comparison with a close relative, Arabidopsis thaliana, revealed 6552 unigenes (4579 upregulated; 1973 downregulated), including 131 Brassica-specific and 116 functionally known floral Arabidopsis homologs. Additionally, 1723, 236 and 232 DEGs were preferentially expressed in the tissues of STs, FB2, and CPs. These DEGs also included 43 transcription factors, mainly AP2/ERF–ERF, NAC, MADS-MIKC, C2H2, bHLH, and WRKY members. The differential gene expression during flower development induced dramatic changes in activities related to metabolic processes (23.7%), cellular (22.7%) processes, responses to the stimuli (7.5%) and reproduction (1%). A relatively large number of DEGs were observed in STs and were overrepresented by photosynthesis-related activities. Subsequent analysis via semiquantitative RT-PCR, histological analysis performed with in situ hybridization of BrLTP1 and transgenic reporter lines (BrLTP promoter::GUS) of B. rapa ssp. pekinensis supported the spatiotemporal expression patterns. Together, these results suggest that a temporally and spatially regulated process of the selective expression of distinct fractions of the same genome leads to the development of floral organs. Interestingly, most of the differentially expressed floral transcripts were located on chromosomes 3 and 9. This study generated a genome expression atlas of the early floral transition to maturation that represented the flowering regulatory elements of Brassica rapa.
KeywordsBrassica rapa Floral organs cDNA microarray Flower development Differential gene expression MADS transcription factors
This study was supported by the Postdoctoral Fellowship Program of the National Institute of Agricultural Science; the Rural Program for Agricultural Science and Technology Development (Project No. PJ01247202); and the Next-Generation Biogreen 21 Program (Project No. PJ01334002), Rural Development Administration, Korea.
SL, JK and MJ conceived and designed the study. MM and MN conducted the bioinformatics analysis, analyzed the data and drafted the manuscript. MM, and SL submitted the array data to the NCBI Gene Expression Omnibus database. SL, JK, JH, ML and MJ revised the manuscript. All the authors agreed on the contents of the paper.
This study was funded by the National Institute of Agricultural Science (Project No. PJ01247202) and Rural Development Administration, Korea (PJ01334002).
Compliance with ethical standards
Conflict of interest
Soo In Lee declares that he has no conflict of interest. Muthusamy Muthusamy declares that he has no conflict of interest. Muhammad Amjad Nawaz declares that he has no conflict of interest. Joon Ki Hong declares that he has no conflict of interest. Myung-Ho Lim declares that he has no conflict of interest. Jin A Kim declares that she has no conflict of interest. Mi-Jeong Jeong declares that she has no conflict of interest.
Data availability statement
The complete set of genome-wide expression data from this study was submitted to the Gene Expression Omnibus database (https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE128989, and the necessary information was also submitted as supplementary data in this article.
- Andrés F, Romera-Branchat M, Martínez-Gallegos R, Patel V, Schneeberger K, Jang S, Altmüller J, Nürnberg P, Coupland G (2015) Floral induction in Arabidopsis thaliana by FLOWERING LOCUS T requires direct repression of BLADE-ON-PETIOLE genes by homeodomain protein PENNYWISE. Plant Physiol 169:2187–2199PubMedPubMedCentralGoogle Scholar
- Bonnema G, Carpio DP, Zhao JJ (2011) Diversity analysis and molecular taxonomy of Brassica vegetable crops. In: Kole C, Sadowski J (eds) Genetics, genomics and breeding of crop plants. Science Publishers, Enfield, NH, pp 81–124Google Scholar
- Honma T, Goto K (2000) The Arabidopsis floral homeotic gene PISTILLATA is regulated by discrete cis-elements responsive to induction and maintenance signals. Dev Camb Engl 127:2021–2030Google Scholar
- Kim S-Y, Park B-S, Kwon S-J, Kim JS, Lim M-H, Park Y-D, Kim DY, Suh S-C, Jin YM, Ahn JH, Lee Y-H (2007) Delayed flowering time in Arabidopsis and Brassica rapa by the overexpression of FLOWERING LOCUS C (FLC) homologs isolated from Chinese cabbage (Brassica rapa L. ssp. pekinensis). Plant Cell Rep 26:327–336CrossRefGoogle Scholar
- Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets brief communication. 33:1870–1874Google Scholar
- Li H, Fan Y, Yu J, Chai L, Zhang J, Jiang J, Cui C, Zheng B, Jiang L, Lu K (2018) Genome-wide identification of flowering-time genes in Brassica species and reveals a correlation between selective pressure and expression patterns of vernalization-pathway genes in Brassica napus. Int J Mol Sci 19:3632CrossRefPubMedPubMedCentralGoogle Scholar
- Liu F, Xiong X, Wu L, Fu D, Hayward A, Zeng X, Cao Y, Wu Y, Li Y, Wu G (2014) BraLTP1, a lipid transfer protein gene involved in epicuticular wax deposition, cell proliferation and flower development in Brassica napus. PLoS ONE 9:1–12Google Scholar
- Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. The Plat Cell 18:1348–1359CrossRefGoogle Scholar
- Wang X, Song H, Sun M, Zhu Z, Xing G, Xu X, Gao M, Hou L, Li M (2017) Digital gene expression analysis during floral transition in pak choi (Brassica rapa subsp. chinensis). Biotechnol Biotechnol Equip 31:670–678Google Scholar
- Xiao D, Zhao JJ, Hou XL, Basnet RK, Carpio DP, Zhang NW, Bucher J, Lin K, Cheng F, Wang XW, Bonnema G (2013) The Brassica rapa FLC homologue FLC2 is a key regulator of flowering time, identified through transcriptional co-expression networks. J Exp Bot 64:4503–4516CrossRefPubMedPubMedCentralGoogle Scholar
- Xu M, Hu T, Zhao J, Park MY, Earley KW, Wu G, Yang L, Poethig RS (2016) Developmental functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) genes in Arabidopsis thaliana. PLoS Genet 12:1–29Google Scholar
- Zhang L, Wang L, Yang Y, Cui J, Chang F, Wang Y, Ma H (2015) Analysis of Arabidopsis floral transcriptome: detection of new florally expressed genes and expansion of Brassicaceae-specific gene families. Front Plant Sci 5:1–11Google Scholar