الفهرس 
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Abstract
The present work was conducted at University of Nebraska-Lincoln, NE, USA. This work included three different research studies. The results of each project could be summarized as follows:
1. Breeding for stem rust resistance in wheat
This study was conducted to understand the genetic basis of stem rust resistance in Nebraska winter wheat. Stem rust seedling resistance was evaluated in two Nebraska winter wheat nurseries, DUP2015 (F6) and TRP2015 (F7) with a total number of 330 genotypes. The DUP2015 nursery was evaluated for stem rust resistance using the common stem rust race in Nebraska “QFCSC” in two replications (one at Lincoln, NE and one at USDA-ARS, in Manhattan, KS). The TRP2015 nursery was evaluated for resistance to races: QFCSC, QTHJC, MCCFC, RCRSC, RKQQC, TPMKC, TTTTF, GFMNC, QCCSM and TTKSK (commonly
known as Ug99) at the USDA Cereal Disease Laboratory in one replication. Genotypes resistant or heterogeneous to race TTKSK were further evaluated with races TTKST, TTTSK and TTKTT, three variants of the Ug99 race group (Newcomb et al., 2016), as well as non-Ug99 races TKTTF and TRTTF that possess significant virulence combinations (Olivera et al., 2012 and Olivera et al., 2015). In addition, the TRP2015 nursery was evaluated for QFCSC race in a second replication at Lincoln, NE. The evaluation was done using Stakman scale (Stakman et al., 1962) and converted to a linear scale. The analysis of variance revealed highly significant differences among the genotypes for the resistance which indicated that our phenotypic assay was successful.
The two nurseries were genotyped for four stem rust genes (Sr31, Sr1RSAmigo, Sr24, and Sr38) at USDA-ARS. Based on the genotyping data, pedigree and the phenotyping data, the two nurseries were postulated to contain five more resistance
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genes; Sr6, Sr36, SrTmp, Sr30, and Sr9e. To corroborate the presence of these genes, SSR markers were used. Out of the 330-tested genotypes, three genotypes contained markers for five stem rust resistance genes and had a very high resistance level against a wide range of stem rust races. In both nurseries, the highest percent of genotypes contained markers for Sr6. Due to these gene pyramids of many stem rust resistance genes in the DUP2105 and TRP2015, it was worth to identify genes with the major effect on stem rust resistance in each nursery by testing the association between resistance to stem rust and the candidate stem rust genes using single marker analysis. In the DUP2015 nursery, two markers Sr24#12 (Sr24) and Xcfd43 (Sr6) had highly significant associations with stem rust resistance with p-values of 0.003 and 0.000000 respectively. Two markers VENTRIUP-LN2 (Sr38) and Xcfd43 (Sr6) had highly significant associations with stem rust resistance in the TRP2015 nursery with p-values of 0.003 and 0.000008, respectively.
Genome-wide association study for stem rust resistance was done on these nurseries using 8905 SNPs and 19 SNPs on chromosome 2D (where Sr6 was mapped) were associated with stem rust seedling resistance. High linkage disequilibrium was found among all the 19 SNPs and the SSR marker for Sr6. Ten gene models were found to be located in the same scaffold with the significant SNPs. Out of these gene models, one gene model was found to have higher expression under disease stress than the favorable conditions. The annotation of this gene has been found to increase the potassium transport in the plant tissue, and hence increases the resistance to the biotic and abiotic stresses. These 19 SNPs should be helpful for marker-assisted selection for this gene.
2. Breeding for common bunt resistance in wheat
This study was conducted at University of Nebraska Lincoln in two locations, Lincoln and Mead to study the resistance to common bunt in winter wheat. Three different nurseries were used in this study, DUP2015 (270 genotypes, F6), TRP2015 (60 genotypes, F7) and Synthetic Turkish lines (25 genotypes). In addition, fourteen common bunt differential lines were used to identify the resistance genes to Nebraska common bunt race. The planting was done on October 14th, 2015 using replicated augmented incomplete block design in two replications. The inoculation was done using Nebraska common race of common bunt using the method of Wilcoxson and Saari (1996). A susceptible check was included to confirm the validation of our test. Despite that the susceptible check revealed low percent of infected heads (17.29 and 11.54% at Lincoln and Mead respectively), a number of six genotypes were very susceptible to common bunt with a percentage of infected heads exceeded 50% which indicated that our infection is valid. Highly significant differences were found among the genotypes for common bunt resistance indicating that breeding for common bunt resistance is possible in the tested genotypes. No significant differences were found between the two locations, so the data was combined, and the average was used. Out of the 355 tested genotypes, eight genotypes were found to be very resistant to common bunt with 0% infected heads, 31 genotypes were found to be resistance with 0.1-5% infected heads and 37 genotypes were found to be moderately resistance with 5.1- 10% infected heads. The remaining genotypes were susceptible
The results of evaluating the differential lines indicating that genes Bt2, Bt3, Bt6, Bt8, Bt9, Bt11, Bt12, Bt13, Btp and Bt15 are completely resistance to Nebraska common bunt race with 0% infected heads. However, Bt1, Bt7 and
Bt10 are partially resistant to this race with infected heads lower than 10%. Genome-wide association study identified eight SNPs on the long arm of chromosome 1A, three SNPs on the long arm of chromosome 1B, one SNP on the long arm of chromosome 4A and one SNP on chromosome 6A to be significantly associated with the resistance (FDR p-value 0.20). Based on the chromosomal location of the previously mapped Bt-genes and the location of the significant SNPs, we can conclude that the significant SNPs which located on chromosome 1B could be Bt1, Bt4, Bt5, Bt6, or Bt12,
Seedling vigour, heading dates, plant height and chlorophyll content were measured in the tested genotypes in order to identify if there is a correlation between common bunt resistance and these traits. No significant correlation was found between the percentage of infected heads and both plant height and heading date in all the three nurseries. A positive significant correlation between the seedling vigour and the percentage of infected heads was found in one nursery (DUP2015) with a value of r = 0.24*. This relationship was not found in the other two nurseries which indicating that seedling vigour cannot be used as an indicator of common bunt susceptibility. Because of the absence of the correlation between the common bunt resistance and the other agronomic traits, the resistance of common bunt seems to be an independent trait which is controlled by its own genetic system. 3. Effect of common bunt infection on some agronomic traits
This study was done at the University of Nebraska Lincoln, Agronomy greenhouses using nine Egyptian spring wheat cultivars. These nine cultivars had never been tested to Nebraska CB race, hence their reaction to this pathotype was unknown, but was expected to be susceptible. As a result of this expectation, two resistance genotypes from the previous study were included in this study in order to identify if there are differences between the response of resistant and susceptible genotypes to common bunt inoculation. The tested cultivars were planted in the greenhouse with two disease treatments, control, and common bunt inoculation, in three replications each in a randomized complete block design (RCBD). The inoculation was done using the method of (Goates, 1996). All the nine Egyptian cultivars were susceptible/very susceptible to Nebraska common bunt race as expected with a percentage of infected heads ranging from 38% - 93%. Seedling vigour, days to heading, chlorophyll content in the flag leaf, plant height, head length, days to maturity, number of tillers/plant, biological yield and root length were measured for all the tested cultivars in both treatments. The results of this study concluded that common bunt infection was found to increase the seedling vigour, delay heading, increase head length, decrease root length and decrease the biological yield in the susceptible genotypes.
Comparing between the response of the susceptible cultivars and resistant genotypes to the common bunt infection, the resistant genotypes were found to have longer roots under the common bunt infection compared with their root length under the control conditions. However, a reduction in the root length was found in some susceptible genotypes due to the common bunt infection. Due to the difficulty in measuring the root length and the different response of the susceptible genotypes, this trait is not a useful trait for the early prediction of
common bunt resistance. However, root length, after being confirmed with additional resistant genotypes, may still be used as a preliminary indicator to identify the resistant genotypes in breeding programs especially when evaluating the genotypes under greenhouse conditions. The absence of the differences between the response of resistant and susceptible genotypes in other agronomic traits confirmed the difficulty of early prediction and selection of common bunt resistance genotypes. Hence the most accurate selection of resistant lines still requires waiting until the end of the growing season to identify resistance.