ORIGINAL ARTICLE Molecular screening of Zymoseptoria tritici resistance genes in wheat (Triticum aestivum L.) using tightly linked simple sequence repeat markers Tilahun Mekonnen & Teklehaimanot Haileselassie & Tanushri Kaul & Manju Sharma & Bekele Geleta & Kassahun Tesfaye Accepted: 21 June 2019 # Koninklijke Nederlandse Planteziektenkundige Vereniging 2019 Abstract Septoria tritici blotch is becoming the major bottleneck to wheat production throughout the world including Ethiopia. Resistance breeding is currently seen as the best strategy, durable, economical and environmen- tally friendly method to control the disease. Nowadays, molecular marker technology is widely used in plant breeding program to promote the speed and efficiency of resistance breeding. So far, several Septoria resistant genes and tightly linked simple sequence repeat markers (SSR) have been identified in wheat. These markers can serve as chromosomal land mark in hunting the resistance genes in diverse breeding materials. However, in Ethio- pia, the application of molecular tools in resistance breed- ing is greatly missing. Therefore, the present study was aimed at searching for Septoria resistant genes (Stb genes) in 180 bread wheat genotypes using 16 tightly linked SSR markers. The result revealed greater degree of genetic variability among the tested genotypes for Stb genes. The genetic frequency of the resistance genes ranged from 6.67% (Stb 8 gene) to 96.1% for stb13 gene. Three wheat genotypes (G21, G63, and G64) possessed the maximum (13) Septoria resistance genes. While 14 of the genotypes were found to have 12 Stb genes. Four genotypes were found to have the minimum (four) Stb genes. The study identified 17 wheat genotypes harbor- ing 12 to 13 Septoria resistance genes. The information is very relevant for breeders in developing broad spectrum and/or durable resistant cultivars through gene pyramiding, and for fast track release of the resistant genotypes to contribute to food and nutritional security in Ethiopia. Keywords Molecular markers . Resistance breeding . Septoria resistance Eur J Plant Pathol https://doi.org/10.1007/s10658-019-01795-y Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10658-019-01795-y) contains supplementary material, which is available to authorized users. T. Mekonnen (*) : T. Haileselassie Institute of Biotechnology, Addis Ababa University, King George VI street, P.O. Box 1176, Addis Ababa, Ethiopia e-mail: mekonnentilahun27@yahoo.com e-mail: tilahun.mekonnen@aau.edu.et T. Kaul Nutritional Improvement of Crops-Plant Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India e-mail: tanushrikaul@gmail.com M. Sharma Amity Institutes of Biotechnology, Amity University Gurgaon, Haryana, India e-mail: sharma.manju131@gmail.com B. Geleta International Maize and Wheat Improvement Center (CIMMYT ), Ethiopia regional office, Addis Ababa, Ethiopia e-mail: b.abeyo@cgiar.org K. Tesfaye Ethiopian Biotechnology Institute. Affiliated with Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia e-mail: kassahuntesfaye@yahoo.com