Journal of Phytopathology. 2017;1–8. wileyonlinelibrary.com/journal/jph | 1 © 2017 Blackwell Verlag GmbH Received: 8 February 2017 | Accepted: 10 April 2017 DOI: 10.1111/jph.12583 ORIGINAL ARTICLE Assessment of genetic diversity of coffee leaf rust pathogen Hemileia vastatrix using SRAP markers Bharathi Kosaraju 1 | Soundararajan Sannasi 2 | Manoj Kumar Mishra 1 | Daivasikamani Subramani 3 | Muniswamy Bychappa 1 1 Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore, Karnataka, India 2 Regional Coffee Research Station, Thandigudi, Dindigul, Tamil Nadu, India 3 Central Coffee Research Institute, Coffee Research Station, Chikmagalur, Karnataka, India Correspondence M. K. Mishra, Plant Biotechnology Division, Unit of Central Coffee Research Institute, Coffee Board, Manasagangothri, Mysore, Karnataka, India. Email: manojmishra.m@gmail.com Abstract Coffee leaf rust caused by the fungus Hemileia vastatrix (Berk and Br.) is a major dis- ease occurring in coffee plantations. Although the rust fungus exists in different physi- ological races, the genetic difference between them is meagrely understood. In this study, genetic diversity of 14 identified and two unidentified leaf rust races was deter- mined 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 frag- ments 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 exist- ence of genetic variability among various leaf rust races and this information will be helpful in coffee breeding programmes. KEYWORDS coffee, genetic variability, Hemileia vastatrix, molecular markers, physiological races 1 | INTRODUCTION Coffee is one of the most important crops in the tropics and considered to be the second most important commodity in the world trade market next to petroleum. The total global production of green coffee is ap- proximately 143.25 million bags (60 kg capacity) with an export earning of over US$ 31.8 billion during 2014. Although more than 100 coffee species are known, only two species, that is, Coffea arabica (known as arabica coffee) and Coffea canephora (known as robusta coffee), are commercially cultivated and consumed. The economy of a number of countries depends heavily on the earnings of this crop.Coffee leaf rust (CLR), popularly known as orange rust, is caused by the biotrophic fungus Hemileia vastatrix Berk. & Br. It is one of the major diseases in coffee species reported in almost all coffee-growing countries of the world. Although both C. arabica and C. canephora are affected by the leaf rust disease, the production and productivity of arabica coffee are severely determined by the incidence level. It has been estimated that in severe incidence level, the yield reduced from 30% to 80% in the case of arabica coffee. Although chemical control of CLR disease by using different fungicides was largely practised in plantation, the use of rust-tolerant coffee genotype was considered to be the most promising alternative (Várzea & Marques, 2005; Zambolim, 2016). In India, coffee breeding aimed for rust resistance has been taken up and continued for the last 80 years, and as a result, many resistant cultivars have been released for commercial cultivation. In the majority of these breeding programmes, tetraploid interspecific hybrids such as Hybrido de Timor (HDT), Devamachy (putative tetraploid hybrid between C. arabica and C. liberica), Ligenioides (spontaneous tetraploid hybrid of C. liberica and Coffea eugenoides) as well as the hybrids obtained from the cross be- tween C. arabica and Coffea canephora are used as the donor parent for