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Background: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. Results: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourddoi:10.21203/rs.3.rs-31351/v2 fatcat:eckfjc52nndjdin2m7ypuqocoi