Relative efficiency of DNA markers (RAPD, ISSR and AFLP) in detecting genetic diversity of bitter gourd (Momordica charantia L.)

Abstract BACKGROUND: Bitter gourd ( Momordica charantia L.) is an important vegetable crop in tropical countries, including China and India. A wide range of genetic diversity exists in India with respect to fruit morphology such as colour, size and exocarp. A diversity assessment conducted using different DNA marker systems amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers) will be helpful in the establishment of a broad‐based description for improved germplasm curation and the identification of germplasm for genome mapping and breeding of bitter gourd. RESULTS: Genetic relationships between 38 bitter gourd accessions were determined with the aid of 29 RAPD, 15 ISSR and six AFLP markers. Greater polymorphism was detected by AFLPs when compared with RAPD and ISSR analyses using the same germplasm array (RAPD 36.5%, ISSR 74.5% and AFLP 78.5% polymorphism). The average marker index (MI) values derived from the three different marker systems differed dramatically, indicating that they vary in their discriminatory power (AFLP > ISSR > RAPD). The AFLP markers used were only weakly correlated with ISSR ( r 2 = 0.007) and RAPD ( r 2 = 0.04) marker analyses, whereas a comparatively high correlation ( r 2 = 0.77) was found between RAPD and ISSR marker systems. CONCLUSION: The studies using RAPD and ISSR markers were not able to uniquely discriminate all the bitter gourd accessions examined, whereas AFLP analysis was discriminatory and allowed for a more complete dissection of unique differences among accessions of bitter gourd within and between collection sites. Copyright © 2007 Society of Chemical Industry