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Genome-wide analysis of structural variation in citrus two varieties related to citrus canker
- 언어ENG
- URLhttps://db.koreascholar.com/Article/Detail/298465
Citrus canker caused by Xanthomonas citri pv. citri is one of economically important diseases in the citrus industry. The devastating bacterial disease results in unattractive quality and a significant reduction in fruit production. Citrus growers and industry in Korea has been struggling with the serious disease causing the prohibition of export market. Korea also became the top import market for oranges. The development of markers linked to citrus canker resistance is strongly needed. In this study, we investigated molecular markers between ‘Kiyomi’ (Citrus unshiu ｘ C. sinensis), a resistant cultivar, and Natsudaidai (C. natsudaidai), a susceptible cultivar. To develop markers, we focused on structural variation (copy number variation, CNV, and presence/absence variation, PAV). It has been well documented that CNV and PAV of defense-related genes are associated with resistant cultivars. Using a read depth approach following next-generation sequencing, we performed genome-wide analysis of CNV and PAV in two varieties. As a result, 633 genes showing at least two times difference between the mapping reads from two varieties and 61 genes showing presence of the mapping reads in only either one of them were screened. Visual inspection using the Integrative Genomics Viewer (IGV) was performed and experimental validation is being investigated. Interestingly, one of PAV candidates showed polymorphism in ‘Kiyomi’ and ‘Natsudaidai’ as well as other resistant and susceptible cultivars. Our results suggest a necessity for the detection of structural variation and indicate that the candidates may be useful for molecular breeding for citrus canker resistance and understanding disease resistance mechanism.
