Wheat (Triticum aestivum L.) is the most widely grown cereal globally and can be grown successfully in many different environments. In USA, it ranks fourth in crop production and first in crop export. Wheat suffers from many different diseases such as common bunt (CB) (Tilletia caries (D.C.) Tul. (=T. tritici) and T. foetida (Wallr.) Liro (=T. laevis)) which can be devastating to wheat yield. Kernels infected by this disease are usually rejected by millers as very low infection rates can result in noticeable odors in flour milled from CB-infected wheat. Fungicides can be used to control common bunt, but they are costly and can not be used in organic fields. In addition, common bunt pathogens has the ability to create fungicide-resistance races. Hence most wheat growers need common bunt resistant cultivars which are developed through breeding programs. Amira Mourad (1),(3), Ahmed Sallam(1),(4), Vikas Belamkar(1), David Hole(2), Richard Little(1), Ezzat Mahdy(3), Bahy R. Bakheit(3) , Atif Abo El-Wafaa(3) and P. Stephen Baenziger (1) (1) Department of Agronomy and Horticulture, Plant Science Hall, UNL, USA (2) Plants, soils and climate department, College of Agricultural and Applied sciences, USU (3) Agronomy Department, Faculty of Agriculture, Assuit University, Egypt (4) Department of Genetics, Faculty of Agriculture, Assuit University, Egypt . pbaennziger1@unl.edu Introduction Genetic Analysis of common bunt resistance in winter bread wheat Objectives The objectives from this study is to (1) study the genetic variation in resistance to common bunt in winter wheat and (2) detect alleles associated resistance to common bunt using GWAS. Materials and methods - 1- Plant materials: All plant materials were sown at Lincoln and Mead. The experimental design was replicated augmented block design with two replications in each location. The plant materials were consist of three populations: a) The differential lines for common bunt were used in this study in order to determine the genes which resist the common race of common bunt in Nebraska. b) Nebraska winter wheat genotypes: 270 F6 lines and 60 F7 experimental lines were used in this study as illustrated in the following scheme . Fig.1. Breeding program of Nebraska winter wheat c) Synthetic Turkish genotypes: a set of 25 Turkish synthetic lines realized at CYMMIT were used in the study 2- Inoculation and phenotyping: All genotypes were inoculated with the common race of common bunt in Nebraska using Goates (1996) method. The scoring was done using Veisz etal. (2000) and Szunics (1990) scale where infected ears 0.0% = very resistant, 0.1–5.0% = resistant, 5.1–10.0% = moderately resistant, 10.1–30.0% = moderately susceptible, 30.1–50.0% = susceptible, 50.1– 100.0% = very susceptible Results 0 5 10 15 20 25 30 35 % infected heads Fig.3. Percentages of infected heads in the differential lines 0 20 40 60 80 100 120 140 160 180 200 Number of genotypes Lincoln Mead y = 0.6156x + 7.2654 R² = 0.3856 0 10 20 30 40 50 60 70 80 0 20 40 60 80 Lincoln Mead Fig.4. Numbers of genotypes representing different degree of resistance at both locations Fig.5. Phenotypic correlation between the common bunt resistance in Lincoln and Mead Fig.6. Manhattan plot for common bunt resistance. The blue line refers to the significant level at false discovery rate(0.20) Fig. 7. The Q–Q plot shows the expected -log (P) versus the -log (P) for common bunt using MLM + kinship References Conclusion SNP ID Chro. Position p value Target allele(1) Allele effect(2) R2(3) M0000420 1AL 151857284 1.05E-04 C:T -5.89 5.4 M0000421 1AL 151857286 1.05E-04 C:A -5.89 5.4 M0000260 1AL 37381806 1.27E-04 A:G -5.09 5.5 M0000406 1AL 134165505 1.68E-04 A:G -4.99 5.0 M0000321 1AL 78836421 2.19E-04 G:C -5.23 4.9 M0001831 2AL 295023013 9.68E-06 A:C -10.6 6.8 M0002334 2BL 123824279 2.10E-04 C:T -11.58 5.6 M0004737 4AL 230764436 1.12E-04 G:A -8.53 5.8 M0005881 5BL 246225902 4.38E-05 T:A -10.01 7.1 M0006180 5BL 415624821 6.88E-05 A:G -11.59 5.3