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Single-molecule real-time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.)

2020-06-30l Hit 1744

Color is an important trait for a fruit and can help grab a consumer’s attention; this fruit color is determined by carotenoid, which ranges from ivory to red. Such modification of color is attributed to the mutation of genes that exist in the carotenoid biosynthetic pathway.

 The research team of Professor Byoung-Cheorl Kang of the Department of Plant Science at Seoul National University investigates the mutation of genes that determine major traits of pepper such as fruit color, identifies the roles and locations of these genes, and utilizes it in the actual breeding field.

 In the study, the Professor Kang’s research team aimed to identify the sequence of the carotenoid biosynthetic gene of capsicum using single-molecule real-time (SMRT) sequencing (Figure 1), as it provides a longer read length and a faster runtime compared with other NGS technologies. The research team found allelic variations of six genes that biosynthesize carotenoid through SMRT.

Figure 1. Schematic diagram of library construction for single-molecule real-time(SMRT) sequencing.

 As a result of analyzing 43 capsicum accession through SMRT and UPLC, most premature stop mutations among six carotenoid biosynthetic genes were revealed as concentrated in two genes (PSY1, CCS). Thus, an analysis was conducted on the correlation between carotenoid profiles and allelic variation shown by the combination of these two genes.
Figure 2. Heatmap of the levels of 10 carotenoids in 43 Capsicum accessions.

 As shown in the Figure 2, the research team summarized carotenoid levels and colors by classifying 43 accessions into four groups based on genotype of accessions. Differences in color of accession and carotenoid level were revealed by each mutation of PSY1 and CCS.

 Through this, they were able to confirm how the mutation of each carotenoid biosynthetic gene affects the color and carotenoid level of a fruit. Furthermore, it was confirmed that SMRT sequencing technology could identify allelic variation of target genes. The allelic variants identified through this study are expected to be utilized in analyzing the breeding of capsicum and carotenoid biosynthesis pathways.

 Although this study took a step forward toward researching the mutation of fruit color of pepper, it was insufficient to explain the mutation of various fruit colors in its entirety. In the meantime, another study recently investigated the presence of a gene that determines the dark fruit color, and another study is being planned to confirm whether this gene could resolve those areas unidentified in this study.

 This study was published in Plant Biotechnology Journal in 2019.

《Professor ByoungCheorl Kang》