Molecular characterization and transcriptome analysis of orange head Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Abstract

The orange head phenotype of Br - or resulted from a large insertion in carotenoid isomerase (BrCRTISO) . Comparative transcriptome analysis revealed that the mutation affected the expression of abundant transcription factor genes. A new orange trait-specific marker was developed for marker-assisted breeding. Orange head leaves are a desirable quality trait for Chinese cabbage. Our previous fine mapping identified BrCRTISO as the Br-or candidate gene for the orange Chinese cabbage mutant. Here, we examined the BrCRTISO gene from white and orange head Chinese cabbage. While BrCRTISO from the white control plant was able to complement the Arabidopsis Atcrtiso mutant phenotype, Brcrtiso with a large insertion from the orange head Chinese cabbage failed to rescue the Arabidopsis mutant phenotype. The results show that Brcrtiso was non-functional, concomitant with the accumulation of prolycopene in Br-or to yield orange head. Comparative transcriptome analysis by RNA-seq identified 372 differentially expressed genes between the control and Br-or mutant using two near-isogenic lines with white and orange inner leaves. The mutation in BrCRTISO specifically affected many genes in the functional groups involved in RNA, protein, transport, and signaling. Particularly, expressions of many transcription factor genes were dramatically altered in Br-or, suggesting a potential role of BrCRTISO or carotenoid metabolites in affecting transcription. A novel co-dominant gene-specific marker was developed that co-segregated with orange color phenotype and would be useful for marker-assisted selection with enhanced selection efficiency. Our study provides new insights into understanding of the molecular basis of Br-or in mediating head leaf color and depicts a global view of the effect of BrCRTISO on cellular processes in plant. It also provides a molecular tool to accelerate breeding new Chinese cabbage cultivars with unique health quality and visual appearance.

Transcriptome Analysis of Orange Head Chinese Cabbage (Brassica rapaL. ssp.pekinensis) and Molecular Marker Development

“…The color of the inner head leaves is usually white, yellow, or orange. The orange color of the inner leaves is a result of the accumulation of prolycopene and other carotenoid pigments [9–11]. In recent years, the orange head Chinese cabbage varieties have gradually captured the attention of breeders and consumers, since they have an attractive color and higher carotenoids compared with the white and yellow head cabbage.…”

“…In recent years, the BrCRTISO (Bra031539) gene has been identified as the Br-or candidate by several research groups. Many insertions/deletions were identified in this gene [9–11, 15], resulting in mutant BrCRTISO proteins, which cannot catalyze the conversion from prolycopene to all- trans -lycopene [15]. Furthermore, studies have also shown mutations of the BrCRTISO gene dramatically alter the expressions of many other genes [11, 15].…”

“…However, controversial results were reported. For example, Su et al [15] found the enzymes are upregulated in the upstream pathway of the all- trans -lycopene biosynthesis and downregulated in the downstream pathway in the orange inner leaves using a RT-qPCR method, while Zhang et al [11] did not observe any expression differentiations of these genes using a RNA-seq technology. In the present study, we employed a high-throughput sequencing method to identify the differentially expressed genes (DEGs) between the orange and white F 2 individuals.…”

Fine mapping and characterization of the or gene in Chinese cabbage (Brassica rapa L. ssp pekinensis)

“…However, a 141-bp deletion in the promoter region and 6-bp deletion, as well as 53 SNPs in the first exon, were found in orangetype cultivars. Zhang et al (2015) compared the genomic sequences of two Chinese cabbage materials and found that their differences included an 88-bp deletion in the promoter region, a 501-bp insertion at the 3' end, and two SNPs. The two SNPs cause two amino acid substitutions and a 501-bp insertion, resulting in the addition of 143 amino acids at the end of BrCRTISO.…”

Sequence Analysis of the Carotenoid Isomerase Gene in Potato (Solanum tuberosum)

“…CRTISO is an important enzyme in carotenoid biosynthesis, catalyzing the prolycopene into lycopene [13]. The genes encoding the CRTISO protein have been isolated in various plant species, including Arabidopsis [3], tomato [4], tobacco [14], and Brassica rapa [15].…”