Hui Feng

Physiological Characterization and Comparative Transcriptome Analysis of a Slow-Growing Reduced-Thylakoid Mutant of Chinese Cabbage (Brassica campestris ssp. pekinensis).

Mutants are ideal for studying physiological processes. The leaves of Chinese cabbage are a major place for photosynthesis, and the mutation of these leaves may directly affect the rate of plant growth and development, thus influencing the formation of its leafy head. We characterized a slow-growing mutant, which was designated as drm. The drm exhibited slow growth and development at the seedling and heading stages, leading to the production of a tiny, leafy head, and chlorophyll-deficient leaves, especially in seedlings. Genetic analysis indicated that the phenotype of drm was controlled by a single recessive nuclear gene. Compared with the wild-type “FT” line, the drms chlorophyll content was significantly reduced and its chloroplast structure was abnormal. Moreover, its photosynthetic efficiency and chlorophyll fluorescence parameters were significantly decreased. The changes in leaf color, combined with these altered physiological characters, may influence the growth and development of plant, ultimately resulting in the slow-growing phenotype. To further understand the molecular regulation mechanisms of phenotypic differences between “FT” and drm, comparative transcriptome analyses were performed using RNA-Seq; a total of 338 differentially expressed genes (DEGs) were detected between “FT” and drm. According to GO and KEGG pathway analysis, a number of DEGs involved in chlorophyll degradation and photosynthesis were identified, such as chlorophyllase and ribulose-1,5-bisphosphate carboxylase/oxygenase. In addition, the expression patterns of 12 DEGs, including three chlorophyll degradation- and photosynthesis-related genes and nine randomly-selected genes, were confirmed by qRT-PCR. Numerous single nucleotide polymorphisms were also identified, providing a valuable resource for research and molecular marker-assistant breeding in Chinese cabbage. These results contribute to our understanding of the molecular regulation mechanisms underlying growth and development and lay the foundation for future genetic and functional genomics in Chinese cabbage.

Comparative transcriptome analysis of the petal degeneration mutant pdm in Chinese cabbage (Brassica campestris ssp. pekinensis) using RNA-Seq.

Flowering, which plays a crucial role in the growth and development of flowering plants, is a crucial point from vegetative growth to reproductive growth. The goal of this study was to examine the differences between the transcriptomes of the Chinese cabbage mutant pdm and the corresponding wild-type line ‘FT’. We performed transcriptome analysis on mRNA isolated from flower buds of pdm and ‘FT’ using Illumina RNA sequencing (RNA-Seq) data. A total of 117 differentially expressed genes (DEGs) were detected. Among the DEGs, we identified a number of genes involved in floral development and flowering, including an F-box protein gene, EARLY FLOWERING 4 (ELF4), and transcription factors BIGPETAL (BPE) and MYB21 (v-myb avian myeloblastosis viral oncogene homolog); differential expression of these genes could potentially explain the difference in the flowers between pdm and ‘FT’. In addition, the expression patterns of 20 DEGs, including 12 floral development and flowering-related genes and eight randomly selected genes, were validated by qRT-PCR, and the results were highly concordant with the RNA-Seq results. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed to better understand the functions of these DEGs. We also identified a large number of single nucleotide polymorphism and insertion/deletion markers, which will be a rich resource for future marker development and breeding research in Chinese cabbage. Also, our analysis revealed numerous novel transcripts and alternative splicing events. The transcriptome analysis provides valuable information for furthering our understanding of the molecular mechanisms that regulate the flowering process, and establishes a solid foundation for future genetic and functional genomic studies in Chinese cabbage.

Identification and validation of a major QTL controlling the presence/absence of leaf lobes in Brassica rapa L.

Leaves are vital plant organs, and a high level of variation in leaf shape, including the leaf lobes, is present in Brassica rapa. Based on a previously-constructed linkage map, QTL analysis of the leaf lobes was performed using the scores from an F2 population during the spring of 2010, and scores from an F2:3 family in the autumn of 2010, respectively. A total of nine QTLs were found to affect leaf lobes. Among these, a major QTL, lob 10.1, was mapped to the bottom of linkage group A10. To develop near iso-genic lines (NILs) for the identified major QTL, an F2 plant without leaf lobes that was homozygous in the targeted region for marker alleles from the male parent (08A061), was backcrossed to 09A001, the recurrent parent with leaf lobes. Two InDel marker loci, BrID10909 and BrID10233, which are closely linked to the major QTL peak position, and 166 SSR and InDel markers from non-targeted chromosomal regions, were used for foreground and background selection, respectively. Three sets of NILs were developed through four cycles of backcrossing followed by two cycles of self-pollination. Compared to 09A001, the recurrent parent, all the NILs showed the absence of leaf lobes and had no significant differences in other agriculturally important traits. NILs are the ideal genetic resource for QTL validation and fine-scale linkage mapping, and, ultimately, gene discovery.