Coffee leaf rust caused by the fungus Hemileia vastatrix (Berk and Br.) is a major disease occurring in coffee plantations. Although the rust fungus exists in different physiological races, the genetic difference between them is meagrely understood. In this study, genetic diversity of 14 identified and two unidentified leaf rust races was determined by sequence‐related amplified polymorphism (SRAP) markers. Of 48 SRAP primer pairs tested, 35 primers are polymorphic and generated 347 distinct scorable fragments. The number of fragments ranged from 4 to 18 with a mean of 9.97 fragments per primer combination. Of the total 347 amplified fragments, 185 fragments (53.31%) are polymorphic with an average of 5.41 fragments per primer combination. The average resolving power (Rp) and the average polymorphism information content (PIC) of the 35 SRAP primer combinations were 13.60 and 0.356, respectively. Of 35 SRAP primer pairs, 15 primer pairs were more informative and generated 25 unique fragments, which are useful for race discrimination. The study demonstrated the existence of genetic variability among various leaf rust races and this information will be helpful in coffee breeding programmes.

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