Development of InDel markers and fingerprinting of bitter gourd (Momordica charantia) based on whole genome re-sequencing

Abstract

Bitter gourd (Momordica charantia) is cultivated widely as a vegetable and herbal medicine in many Asian and African countries. Two varieties ('LS-5' and 'LS-22') were re-sequenced by next-generation sequencing technology, and a set of InDel markers was developed. The genome of 'Dali-11' was the reference genome. Exactly 59098 and 73683 InDel loci were identified in 'LS-5' and 'LS-22', respectively. To verify the reliability of this set of InDel markers, 220 pairs of InDel primers were designed and synthesised. Primers were preliminarily detected by 8% polyacrylamide gel electrophoresis. Thereafter, 15 pairs of polymorphic primers were selected and employed to construct the DNA fingerprint of 27 bitter gourd varieties. The purity of five hybrid seed lots, 'Zhongyu', 'Heiyu', 'Lvzhu', 'Shunliu 3' and 'Shunliu 8', was determined using the specific primers. In this study, a batch of InDel primers with high polymorphism potential was developed based on resequencing. These primers can effectively distinguish some bitter gourd varieties. Therefore, this set of reliable and accurate InDel markers can provide a richer marker source for bitter gourd variety identification and seed purity determination.