Although phenotyping for stem rust resistance is routinely performed for all populations each year, but the emergence of new races and weather conditions could affect the progress of selection.
In this program, thousands of crosses are made followed by phenotyping and genotyping to select the most promising genotypes for future breeding program. The winter wheat breeding program in the University of Nebraska-Lincoln aims to select and produce wheat cultivars having high yield attributes, winter survival, disease resistance (including stem rust) and end-use quality ( Baenziger et al., 2001). Although there have been many research efforts to understand the genetic control of this race, further studies are needed to reveal major and minor genes controlling the resistance against this race ( Mourad AMI. In Nebraska and the United States, QFCSC has been reported as the predominant stem rust race ( Jin 2005). To date, more than 80 stem rust (Sr) genes have been described in tetraploid and hexaploid wheat, and their wild relatives, (online Sr gene catalog, Singh, 2017). graminis), identifying stable sources of resistance, reducing potential new races in the population, and monitoring potential new races of the pathogen through a global network ( Kolmer 1996 Hartman et al., 2016). due to the successful national barberry ( Berberis vulgaris L.) eradication program (the alternate host for P. In recent years, stem rust losses have been minor in the U.S. tritici (Pgt) Erikss and Henning, has been devastating to wheat ( Triticum aestivum L.) through many decades of production especially during the 1950s in the United States( Leonard 2001 Leonard and Szabo 2005). As a result, 23 genotypes were considered as the most suitable parents for crossing to produce highly resistant stem rust genotypes against the QFCSC. To select the most promising stem rust resistant genotypes, a new approach was suggested based on four criteria including, phenotypic selection, number of resistant allele(s), the genetic distance among the selected parents, and number of the different resistant allele(s) in the candidate crosses. The LD analysis between SNPs located on 2A and Sr38 gene reveal high significant LD genomic regions which was previously reported. Highly significant LD was found among these 59 significant SNPs on chromosome 2A and 12 significant SNPs with an unknown chromosomal position. Promising high linkage disequilibrium (LD) genomic regions were found in all chromosomes except 2B which suggested they include candidate genes controlling stem rust resistance. A set of 11,911 single-nucleotide polymorphism (SNP) markers was used to perform GWAS which detected 84 significant marker-trait associations (MTAs) with SNPs located on chromosomes 1B, 2A, 2B, 7B and an unknown chromosome. While 28 genotypes (13.2%) were susceptible to stem rust. The results indicated that 184 genotypes (86.8%) had different degrees of resistance to this common race. At the seedling stage, the reaction of the common stem rust race QFCSC in Nebraska was measured in a set of 212 genotypes from F 3:6 lines. Seedling screening and genome-wide association study (GWAS) were used to determine the genetic diversity of wheat genotypes obtained on stem rust resistance loci. The production and cultivation of genetically resistant cultivars are one of the most successful and environmentally friendly ways to protect wheat against fungal pathogens. is an important disease of common wheat globally. 5Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, Egypt.4Department of Plant Pathology, University of Nebraska–Lincoln, Lincoln, NE, United States.3Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States.2Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt.1Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat, Egypt.Stephen Baenziger 3, Stephen Wegulo 4, Vikas Belamkar 3 and Ahmed Sallam 5*