Correction: 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.

[This corrects the article DOI: 10.1371/journal.pone.0191297.].

Transcriptome analysis reveals important candidate genes involved in grain-size formation at the stage of grain enlargement in common wheat cultivar "Bainong 4199".

Grain-size is one of the yield components, and the first 14 days after pollination (DAP) is a crucial stage for wheat grain-size formation. To understand the mechanism of grain-size formation at the whole gene expression level and to identify the candidate genes related to grain pattern formation, cDNA libraries from immature grains of 5 DAP and 14 DAP were constructed. According to transcriptome analysis, a total of 12,555 new genes and 9,358 differentially expressed genes (DEGs) were obtained. In DEGs, 2,876, 3,357 and 3,125 genes were located on A, B and D subgenome respectively. 9,937 (79.15%) new genes and 9,059 (96.80%) DEGs were successfully annotated. For DEGs, 4,453 were up-regulated and 4,905 were down-regulated at 14 DAP. The Gene Ontology (GO) database indicated that most of the grain-size-related genes were in the same cluster. The Kyoto Encyclopedia of Genes and Genomes (KEGG) database analysis showed that 130, 129 and 20 DEGs were respectively involved in starch and sucrose metabolism, plant hormone signal transduction and ubiquitin-mediated proteolysis. Expression levels of 8 randomly selected genes were confirmed by qRT-PCR, which was consistent with the transcriptome data. The present database will help us understand the molecular mechanisms underlying early grain development and provide the foundation for increasing grain-size and yield in wheat breeding programs.

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.

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.