Molecular Diversity Among Bitter Melon (Momordica charantia L.) Genotypes Using SSRs and SNPs

Bitter melon (syn. bitter gourd, balsam pear, snap melon; Momordica charantia L; Family Cucurbitaceae; 2n = 22) is grown traditionally in the tropical and subtropical areas of Asia, the Amazon, east Africa, and the Caribbean as food vegetable and medicine. Bitter melon is the most extensively used food crop for prevention and cure of cancer and diabetes. The cultivation and consumption of the fruit and fruit extracts of bitter melon are becoming increasingly popular now in the US. Presently, it is grown in at least eight states (AL, CT, FL, HI, LA, PA, TX and KY) of the US and also in Puerto Rico and the Virgin Islands. In the recent past, molecular markers including random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (IISR) and amplified fragment length polymorphism (AFLP) markers have been used to evaluate genetic diversity in bitter melon. However, no microsatellite or SSR (simple sequence repeat markers) has been developed in this crop. To fill this gap, we recently sequenced cDNA made from the RNA of fruit tissue and obtained 193596 reads using Illumina 2000 HiSeq and identified 1203 sequences containing di and tri microsatellite motifs. In addition to this, we have collected 96 varieties of diverse pedigree and geographical origin (India, China, Japan, Thailand, Taiwan and Hong Kong) and identified SNPs using GBS (Genotyping by sequencing) technology. Observations recorded on six fruit characters including color (white vs. green), shape (long vs. round), surface (spiny vs. non-spiny), size (large vs. small) and bitterness (bitter vs. less-bitter) revealed contrasting variation among the accessions.