Stem rust (caused by Puccinia graminis f. sp. tritici Erikss. & E. Henn.), is a major disease in wheat (Triticum aestivium L.). However, in recent years it occurs rarely in Nebraska due to weather and the effective selection and gene pyramiding of resistance genes. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, we applied genome-wide association study (GWAS) on a set of 270 winter wheat genotypes (A-set). Genotyping was carried out using genotyping-by-sequencing and ∼35,000 high-quality SNPs were identified. The tested genotypes were evaluated for their resistance to the common stem rust race in Nebraska (QFCSC) in two replications. Marker-trait association identified 32 SNP markers, which were significantly (Bonferroni corrected P < 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of Sr6 gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD, r2) was found between the significant SNPs and the specific SSR marker for the Sr6 gene (Xcfd43). This suggests the significant SNP markers are tagging Sr6 gene. Out of the 32 significant SNPs, eight SNPs were in six genes that are annotated as being linked to disease resistance in the IWGSC RefSeq v1.0. The 32 significant SNP markers were located in nine haplotype blocks. All the 32 significant SNPs were validated in a set of 60 different genotypes (V-set) using single marker analysis. SNP markers identified in this study can be used in marker-assisted selection, genomic selection, and to develop KASP (Kompetitive Allele Specific PCR) marker for the Sr6 gene.HighlightsNovel SNPs for Sr6 gene, an important stem rust resistant gene, were identified and validated in this study. These SNPs can be used to improve stem rust resistance in wheat.

BackgroundCommon bunt (caused by Tilletia caries and T. foetida) has been considered as a major disease in wheat (Triticum aestivum) following rust (Puccinia spp.) in the Near East and is economically important in the Great Plains, USA. Despite the fact that it can be easily controlled using seed treatment with fungicides, fungicides often cannot or may not be used in organic and low-input fields. Planting common bunt resistant genotypes is an alternative.ResultsTo identify resistance genes for Nebraska common bunt race, the global set of differential lines were inoculated. Nine differential lines carrying nine different genes had 0% infected heads and seemed to be resistant to Nebraska race. To understand the genetic basis of the resistance in Nebraska winter wheat, a set of 330 genotypes were inoculated and evaluated under field conditions in two locations. Out of the 330 genotypes, 62 genotypes had different degrees of resistance. Moreover, plant height, chlorophyll content and days to heading were scored in both locations. Using genome-wide association study, 123 SNPs located on fourteen chromosomes were identified to be associated with the resistance. Different degrees of linkage disequilibrium was found among the significant SNPs and they explained 1.00 to 9.00% of the phenotypic variance, indicating the presence of many minor QTLs controlling the resistance.ConclusionBased on the chromosomal location of some of the known genes, some SNPs may be associated with Bt1, Bt6, Bt11 and Bt12 resistance loci. The remaining significant SNPs may be novel alleles that were not reported previously. Common bunt resistance seems to be an independent trait as no correlation was found between a number of infected heads and chlorophyll content, days to heading or plant height.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1435-x) contains supplementary material, which is available to authorized users.

Stem rust (caused by Puccinia graminis f. sp. tritici ) is a major disease of wheat. To understand the genetic basis of stem rust resistance in Nebraska winter wheat, a set of 330 genotypes representing two nurseries (DUP2015 and TRP2015) were evaluated for resistance to a Nebraska stem rust race (QFCSC) in two replications. The TRP2015 nursery was also evaluated for its resistance to an additional 13 stem rust races. The analysis of variance revealed significant variation among genotypes in both populations for stem rust resistance. Nine stem rust genes, Sr6 , Sr31 , Sr1RS Amigo , Sr 2 4 , Sr36 , SrTmp , Sr7b , Sr9b , and Sr38 , were expected and genotyped using gene-specific markers. The results of genetic analysis confirmed the presence of seven stem rust resistance genes. One genotype (NE15680) contained targ et alleles for five stem rust resistance genes and had a high level of stem rust resistance against different races. Single marker analysis indicated that Sr24 and Sr38 were highly significantly associated with stem rust resistance in the DUP2015 and TRP2015 nurseries, respectively. Linkage disequilibrium analysis identified the presence of 17 SNPs in high linkage with the Sr38 -specific marker. These SNPs potentially tagging the Sr38 gene could be used in marker-assisted selection after validating them in additional genetic backgrounds.

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Experiments involving the intercropping faba bean with each of lupin, fenugreek and Egyptian clover as well as growing faba bean alone were carried out at Assiut University on a farm naturally infested with Orobanche in two seasons. The major objective of the study was to investigate the effect of different intercropping combinations with faba bean on the infestation with Orobanche. The results obtained revealed that intercropping faba bean with each of lupin, fenugreek and Egyptian clover markedly reduced the Orobanche crenata Forsk infestation of faba bean. the number of branches, the height of the first pod, the number of pods, the seed yield and the number and dry weight of Orobanche spikes were significantly affected by the intercropping treatments, but these had no significant influence on plant height, straw yield or 100-seed weight. intercropping faba bean with each of lupin, fenugreek and Egyptian clover increased the faba bean seed yield, consequently the economic return was also increased.

Modified mass and family selection for seed yield production of berseem clover {Trifohuni alexandrmiini L.) cv. 'I'ahl' were applied for two generations. Two hundred plants (5 % intensity of selection) were selected for seed yield in the first season, 1985/86. In the second season, 1986/87, selection between and within half-sib families was practiced. In addition, equal parts of seeds from each of the 200 selected plants were bulked to form the Ci modified mass selection; after establishing, the same procedure was adopted to form the C2 generation. The cycles 1 and 2 of half-sib families and modified mass selection along with the base population family were evaluated for forage and seed yields. The realized gains from modified mass selection were 6.03 and 9.51 % for fresh forage yield, 5.57 and 10.86 % for protein yield and 13.23 and 16.19 % for seed yield in cycles 1 and 2, respectively, over the base population. The realized gain from family selection in cycle 2 as a percentage of the base population mean amounted to 11.32, 13.35, 17.47 and 3.15% for forage, protein, and seed yield and seed index, respectively.The broad sense heritability, as estimated from the variance components was 89.63, 63.03, and 76.67 % for dry forage, seed yield and seed index, respectively.Although, all these five traits (fresh, dry, protein, and seed yield and seed index) had positive correlation with each other, weak correlations were found between seed yield and forage yields. Furthermore, close associations were found among forage yield traits.

Fifty‐six accessions of multi‐cut Egyptian clover were compared at four experiments under different environmental conditions; i.e. location and season. Considerable variation existed for all the characters studied. The genetic variance exceeded the environmental variance for all the studied traits. Heritability was high for all characters studied. The expected genetic advance from selection of the superior 10.7% of the accessions as calculated from the combined data reached to 16.10, 17.50, 5.20, 20.60, 3.52 and 21.00 for mean plant height, seasonal fresh forage yield, mean dry matter percentage, seasonal dry forage yield, mean protein percentage, and seasonal protein yield, respectively. Both phenotypic and genotypic correlations among traits showed that mean plant height was positively correlated with each of seasonal fresh forage yield, seasonal dry forage yield, mean dry matter percentage and seasonal protein yield, but negatively correlated with mean protein percentage. Negative correlation were also found between mean protein percentage with seasonal fresh and dry forage yield. Over all experiments, pat‐coefficient analysis revealed that seasonal fresh forage yield had the highest positive direct effect on seasonal protein yield (0.841), followed by mean dry matter percentage (0.461). The mean protein percentage showed the minimum direct (0.172) and indirect influence on seasonal protein yield.

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