Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for \u3ci\u3eSr6\u3c/i\u3e Stem Rust Resistance Gene in Bread Wheat

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 \u3c 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

Registration of ‘NE05548’ (Husker Genetics Brand Panhandle) Hard Red Winter Wheat

Western Nebraska wheat producers and those in adjacent areas want taller wheat (Triticum aestivum L.) cultivars that retain their height under drought for better harvestability. ‘NE05548’ (Reg. No. CV-1117, PI 670462) hard red winter wheat was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA-ARS and released in January 2014 by the developing institutions. NE05548 was released primarily for its superior performance under rainfed conditions in western Nebraska and adjacent areas of the Great Plains and its tall plant stature. NE05548 was selected from the cross NE97426/NE98574 made in 1999 where the pedigree of NE97426 is ‘Brigantina’/2*‘Arapahoe’ and the pedigree of NE98574 is CO850267/‘Rawhide’. The F1 generation was grown in the greenhouse in 2000, and the F2 to F3 generations were advanced using the bulk breeding method in the field at Mead, NE, in 2001 to 2002. In 2003, single F3–derived F4 head rows were grown for selection. There was no further selection thereafter. The F3:5 was evaluated as a single four-row plot at Lincoln, NE, and a single row at Mead, NE, in 2004. In 2005, it was assigned the experimental line number NE05548. NE05548 was evaluated in replicated trials thereafter. It has excellent winter survival, acceptable disease reactions to many of the common diseases in its target area, and acceptable end-use quality for bread making

Registration of ‘NE05548’ (Husker Genetics Brand Panhandle) Hard Red Winter Wheat

Western Nebraska wheat producers and those in adjacent areas want taller wheat (Triticum aestivum L.) cultivars that retain their height under drought for better harvestability. ‘NE05548’ (Reg. No. CV-1117, PI 670462) hard red winter wheat was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA-ARS and released in January 2014 by the developing institutions. NE05548 was released primarily for its superior performance under rainfed conditions in western Nebraska and adjacent areas of the Great Plains and its tall plant stature. NE05548 was selected from the cross NE97426/NE98574 made in 1999 where the pedigree of NE97426 is ‘Brigantina’/2*‘Arapahoe’ and the pedigree of NE98574 is CO850267/‘Rawhide’. The F1 generation was grown in the greenhouse in 2000, and the F2 to F3 generations were advanced using the bulk breeding method in the field at Mead, NE, in 2001 to 2002. In 2003, single F3–derived F4 head rows were grown for selection. There was no further selection thereafter. The F3:5 was evaluated as a single four-row plot at Lincoln, NE, and a single row at Mead, NE, in 2004. In 2005, it was assigned the experimental line number NE05548. NE05548 was evaluated in replicated trials thereafter. It has excellent winter survival, acceptable disease reactions to many of the common diseases in its target area, and acceptable end-use quality for bread making

Registration of ‘NH03614 CL’ Wheat

‘NH03614 CL’ (Reg. No. CV-1051, PI 653833) hard red winter wheat (Triticum aestivum L.) was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA-ARS and released in 2008 by the developing institutions and the South Dakota Agricultural Experiment Station and the Wyoming Agricultural Experiment Station. In addition to researchers at the releasing institutions, USDA-ARS researchers at Manhattan, KS and St. Paul, MN participated in the development of NH03614 CL. NH03614 CL was selected from the cross ‘Wesley’ sib//‘Millennium’ sib/‘Above’ sib that was made in the spring of 1997 to develop new herbicide-tolerant cultivars. NH03614 CL was selected using the bulk breeding method as an F3:4 line (F3–derived line in the F4 generation) in 2001, and in 2003 was assigned experimental line number NH03164. NH03614 CL was released primarily for its herbicide tolerance to imadazolinone compounds which control many previously diffi cult-to-control weeds in wheat production systems, and for its superior adaptation to rainfed wheat production systems in Nebraska, Wyoming, South Dakota, and counties in adjacent states

Incidence of \u3ci\u3eWheat streak mosaic virus, Triticum mosaic virus\u3c/i\u3e, and \u3ci\u3eWheat mosaic virus\u3c/i\u3e in Wheat Curl Mites Recovered from Maturing Winter Wheat Spikes

Wheat curl mites (WCM; Aceria tosichella) transmit Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and Wheat mosaic virus (WMoV) to wheat (Triticum aestivum L.) in the Great Plains region of the United States. These viruses can be detected in single, double, or triple combinations in leaf samples. Information on incidence of viruses inWCM at the end of the growing season is scant. The availability of this information can enhance our knowledge of the epidemiology ofWCM-transmitted viruses. This research was conducted to determine the frequency of occurrence of WSMV, TriMV, and WMoV in WCM populations on fieldcollected maturing wheat spikes and to determine differences in WCM densities in three geographical regions (southeast, west-central, and panhandle) in Nebraska. Maturing wheat spikes were collected from 83 fields across Nebraska in 2011 and 2012. The spikes were placed in proximity to wheat seedlings (three- to four-leaf stage) inWCM-proof cages in a growth chamber and on sticky tape.WCM that moved off the drying wheat spikes in cages infested the wheat seedlings. WCM that moved off wheat spikes placed on sticky tape were trapped on the tape and were counted under a dissecting microscope. At 28 days after infestation, the wheat plants were tested for the presence ofWSMV, TriMV, orWMoV using enzyme-linked immunosorbent assay and multiplex polymerase chain reaction. WSMV was the most predominant virus detected in wheat seedlings infested with WCM from field-collected spikes. Double (TriMV+WSMV or WMoV+WSMV) or triple (TriMV+ WMoV +WSMV) virus detections were more frequent (47%) than single detections (5%) of TriMV or WSMV. Overall, 81% of the wheat seedlings infested with WCM tested positive for at least one virus. No significant association (P \u3e 0.05) was found between regions for WCM trapped on tape. These results suggest that WCM present on mature wheat spikes harbor multiple wheat viruses and may explain high virus incidence when direct movement of WCM into emerging winter wheat occurs in the fall

Quantification of Yield Loss Caused by \u3ci\u3eTriticum mosaic virus\u3c/i\u3e and \u3ci\u3eWheat streak mosaic virus\u3c/i\u3e in Winter Wheat Under Field Conditions

Triticum mosaic virus (TriMV) and Wheat streak mosaic virus (WSMV) infect winter wheat (Triticum aestivum) in the Great Plains region of the United States. The two viruses are transmitted by wheat curl mites (Aceria tosichella), which also transmit High Plains virus. In a field study conducted in 2011 and 2012, winter wheat cultivars Millennium (WSMV-susceptible) and Mace (WSMV-resistant) were mechanically inoculated with TriMV, WSMV, TriMV+WSMV, or sterile water at the two-leaf growth stage. Chlorophyll meter (soil plant analysis development [SPAD]) readings, area under the SPAD progress curve (AUSPC), grain yield (=yield), yield components (spikes/m2, kernels/spike, 1,000-kernel weight), and aerial dry matter were determined. In Millennium, all measured variables were significantly reduced by single or double virus inoculation, with the greatest reductions occurring in the double-inoculated treatment. Among the yield components, the greatest reductions occurred in spikes/m2. In Mace, only AUSPC was significantly reduced by the TriMV+WSMV treatment in 2012. There was a significant (P ≤ 0.05), negative linear relationship between SPAD readings and day of year in all inoculation treatments in Millennium and in the TriMV+WSMV treatment in Mace. There were significant (P ≤ 0.05), positive linear relationships between yield and SPAD readings and between yield and aerial dry matter in Millennium but not in Mace. The results from this study indicate that under field conditions, (i) Mace, a WSMV-resistant cultivar, is also resistant to TriMV, and (ii) double inoculation of winter wheat by TriMV and WSMV exacerbates symptom expression and yield loss in a susceptible cultivar

Effects of Single and Double Infections of Winter Wheat by \u3ci\u3eTriticum mosaic virus\u3c/i\u3e and \u3ci\u3eWheat streak mosaic virus\u3c/i\u3e on Yield Determinants

Triticum mosaic virus (TriMV) is a recently discovered virus infecting wheat (Triticum aestivum) in the Great Plains region of the United States. It is transmitted by wheat curl mites (Aceria tosichella) which also transmit Wheat streak mosaic virus (WSMV) and Wheat mosaic virus. In a greenhouse study, winter wheat ‘Millennium’ (WSMV susceptible) and ‘Mace’ (WSMV resistant) were mechanically inoculated with TriMV, WSMV, TriMV+WSMV, or sterile water at the two-leaf growth stage. At 28 days after inoculation, final chlorophyll meter (soil plant analysis development [SPAD]) readings, area under the SPAD progress curve (AUSPC), the number of tillers per plant, shoot and root weight, and total nitrogen and carbon content were determined. In Millennium, all measured variables were significantly reduced by single or double virus infections, with the greatest reductions occurring in the double-infection treatment. In Mace, only final SPAD readings, AUSPC, and total nitrogen were significantly reduced by single or double virus infections. There was a significant (P ≤ 0.05), positive linear relationship between SPAD readings and shoot weight in Millennium but not in Mace. The relationship between total nitrogen and shoot weight was positive, linear, and significant in both cultivars. The results from this study indicate that Mace, a WSMV-resistant cultivar, is also resistant to TriMV, and double infection of winter wheat by TriMV and WSMV exacerbates symptom expression and loss of biomass in susceptible cultivars

Occurrence and Distribution of \u3ci\u3eTriticum mosaic virus\u3c/i\u3e in the Central Great Plains

Wheat curl mite (WCM)-transmitted viruses—namely, Wheat streak mosaic virus (WSMV), Triticum mosaic virus (TriMV), and the High Plains virus (HPV)—are three of the wheat-infecting viruses in the central Great Plains of the United States. TriMV is newly discovered and its prevalence and incidence are largely unknown. Field surveys were carried out in Colorado, Kansas, Nebraska, and South Dakota in spring and fall 2010 and 2011 to determine TriMV prevalence and incidence and the frequency of TriMV co-infection with WSMV or HPV in winter wheat. WSMV was the most prevalent and was detected in 83% of 185 season–counties (= s-counties), 73% of 420 season– fields (= s-fields), and 35% of 12,973 samples. TriMV was detected in 32, 6, and 6% of s-counties, s-fields, and samples, respectively. HPV was detected in 34, 15, and 4% of s-counties, s-fields, and samples, respectively. TriMV was detected in all four states. In all, 91% of TriMV-positive samples were co-infected with WSMV, whereas WSMV and HPV were mainly detected as single infections. The results from this study indicate that TriMV occurs in winter wheat predominantly as a double infection with WSMV, which will complicate breeding for resistance to WCM-transmitted viruses

Effects of Integrating Cultivar Resistance and Fungicide Application on Fusarium Head Blight and Deoxynivalenol in Winter Wheat

Fusarium head blight (FHB) or scab, incited by Fusarium graminearum, can cause significant economic losses in small grain production. Five field experiments were conducted from 2007 to 2009 to determine the effects on FHB and the associated mycotoxin deoxynivalenol (DON) of integrating winter wheat cultivar resistance and fungicide application. Other variables measured were yield and the percentage of Fusarium-damaged kernels (FDK). The fungicides prothioconazole + tebuconazole (formulated as Prosaro 421 SC) were applied at the rate of 0.475 liters/ha, or not applied, to three cultivars (experiments 1 to 3) or six cultivars (experiments 4 and 5) differing in their levels of resistance to FHB and DON accumulation. The effect of cultivar on FHB index was highly significant (P \u3c 0.0001) in all five experiments. Under the highest FHB intensity and no fungicide application, the moderately resistant cultivars Harry, Heyne, Roane, and Truman had less severe FHB than the susceptible cultivars 2137, Jagalene, Overley, and Tomahawk (indices of 30 to 46% and 78 to 99%, respectively). Percent fungicide efficacy in reducing index and DON was greater in moderately resistant than in susceptible cultivars. Yield was negatively correlated with index, with FDK, and with DON, whereas index was positively correlated with FDK and with DON, and FDK and DON were positively correlated. Correlation between index and DON, index and FDK, and FDK and DON was stronger in susceptible than in moderately resistant cultivars, whereas the negative correlation between yield and FDK and yield and DON was stronger in moderately resistant than in susceptible cultivars. Overall, the strongest correlation was between index and DON (0.74 ≤ R ≤ 0.88, P ≤ 0.05). The results from this study indicate that fungicide efficacy in reducing FHB and DON was greater in moderately resistant cultivars than in susceptible ones. This shows that integrating cultivar resistance with fungicide application can be an effective strategy for management of FHB and DON in winter wheat

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for \u3ci\u3eSr6\u3c/i\u3e Stem Rust Resistance Gene in Bread Wheat

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 \u3c 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