RNA-seq transcriptome analysis of the immature seeds of two Brassica napus lines with extremely different thousand-seed weight to identify the candidate genes related to seed weight

Xinxin Geng; Na Dong; Yuquan Wang; Gan Li; Lijun Wang; Xuejiao Guo; Jiabing Li; Zhaopu Wen; Wenhui Wei

doi:10.1371/journal.pone.0191297

RNA-seq transcriptome analysis of the immature seeds of two Brassica napus lines with extremely different thousand-seed weight to identify the candidate genes related to seed weight

PLoS One. 2018 Jan 30;13(1):e0191297. doi: 10.1371/journal.pone.0191297. eCollection 2018.

Authors

Xinxin Geng^{1

2

3}, Na Dong¹, Yuquan Wang¹, Gan Li¹, Lijun Wang², Xuejiao Guo¹, Jiabing Li¹, Zhaopu Wen¹, Wenhui Wei^{1

2}

Affiliations

¹ College of Life Science and Technology, Henan Institute of Science and Technology / Collaborative Innovation Center of Modern Biological Breeding, Henan Province, Xinxiang, China.
² Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.
³ Applied Biotechnology Center, Wuhan Institute of Bioengineering, Wuhan, China.

Abstract

Brassica napus is an important oilseed crop worldwide. Although seed weight is the main determinant of seed yield, few studies have focused on the molecular mechanisms that regulate seed weight in B. napus. In this study, the immature seeds of G-42 and 7-9, two B. napus doubled haploid (DH) lines with extremely different thousand-seed weight (TSW), were selected for a transcriptome analysis to determine the regulatory mechanisms underlying seed weight at the whole gene expression level and to identify candidate genes related to seed weight. A total of 2,251 new genes and 2,205 differentially expressed genes (DEGs) were obtained via RNA-seq (RNA sequencing). Among these genes, 1,747 (77.61%) new genes and 2020 (91.61%) DEGs were successfully annotated. Of these DEGs, 1,118 were up-regulated and 1,087 were down-regulated in the large-seed line. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis indicated that 15 DEGs were involved in ubiquitin-mediated proteolysis and proteasome pathways, which might participate in regulating seed weight. The Gene Ontology (GO) database indicated that 222 DEGs were associated with the biological process or molecular function categories related to seed weight, such as cell division, cell size and cell cycle regulation, seed development, nutrient reservoir activity, and proteasome-mediated ubiquitin-dependent protein catabolic processes. Moreover, 50 DEGs encoding key enzymes or proteins were identified that likely participate in regulating seed weight. A DEG (GSBRNA2T00037121001) identified by the transcriptome analysis was also previously identified in a quantitative trait locus (QTL) region for seed weight via SLAF-seq (Specific Locus Amplified Fragment sequencing). Finally, the expression of 10 DEGs with putative roles in seed weight and the expression of the DEG GSBRNA2T00037121001 were confirmed by a quantitative real-time reverse transcription PCR (qRT-PCR) analysis, and the results were consistent with the RNA sequencing data. This work has provided new insights on the molecular mechanisms underlying seed weight-related biosynthesis and has laid a solid foundation for further improvements to the seed yield of oil crops.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brassica napus / genetics*
Brassica napus / growth & development*
Gene Expression Profiling*
Molecular Sequence Annotation
Seeds / genetics*
Seeds / growth & development*
Sequence Analysis, RNA*

Grants and funding

This work was funded by the National Natural Science Foundation of China (grant no. 31371664), the Scientific and Technological Project of Wuhan City (grant no. 2013020501010174) and the National Nonprofit Institute Research Grant (grant no. 1610172012001). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.