Genotyping-by-sequencing (GBS) is a genetic screening method for discovering and genotyping novel... more Genotyping-by-sequencing (GBS) is a genetic screening method for discovering and genotyping novel single nucleotide polymorphisms (SNPs) in crop genomes and populations. In the current research a phenotypic and genotypic assessment of 76 durum wheat (Triticum durum Desf.) accessions of Azerbaijan origin was made using six phenotypic traits and GBS technology. After screening for leaf and stem rust resistance at the seedling stage, 16 genotypes displayed resistance to leaf rust and 14 to stem rust. Some relationships were found between resistance to leaf rust and phenotypic traits of botanical varieties. The highest Pearson’s correlation (r=0.53; p < 0.001) was noted between awn color and pubescence. The durum wheat genotypes fell into four main groups in the clustered heat map; grouping according to botanical variety. A total of 748 SNP markers were obtained for the collection. The average polymorphic information content and genetic diversity index for the entire collection were ...
With climate variation common in the U.S. Great Plains and particularly in Nebraska, wheat grower... more With climate variation common in the U.S. Great Plains and particularly in Nebraska, wheat growers prefer broadly adapted cultivars. ‘NE10589’ (Reg. no. CV‐1165, PI 675998) hard red winter wheat (Triticum aestivum L.) was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA–ARS and released in January 2015 by the developing institutions. NE10589 was released primarily as a broadly adapted semi‐dwarf cultivar for its superior performance under rainfed conditions throughout Nebraska and adjacent areas of the Great Plains. Its broad adaptation ensures that it will perform well under the typical environmental fluctuations that occur in Nebraska. NE10589 was selected from the cross ‘OK98697’/‘Jagalene’//‘Camelot’, where the pedigree of OK98697 is ‘TAM 200’/‘HBB313E’//‘2158’. The F2 to F3 generations were advanced using the bulk breeding method at the Eastern Nebraska Research and Extension Center near Mead, NE, in 2006–2007. In 2007–2008, single F3:4 head ...
f. sp.() causes wheat stem rust, a devastating fungal disease. Theresistance gene confers immunit... more f. sp.() causes wheat stem rust, a devastating fungal disease. Theresistance gene confers immunity against this pathogen's most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and naturalisolates to identify a fungal gene namedthat is required foravirulence. Thegene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin ofisolates virulent onis associated with the nonfunctionalization of thegene by the insertion of a mobile element. The discovery ofprovides a new tool forsurveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.
Western Nebraska wheat producers and those in adjacent areas want taller wheat (Triticum aestivum... more 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 furth...
Resistance to the Ug99 group of races of the stem rust fungus Puccinia graminis f. sp. tritici is... more Resistance to the Ug99 group of races of the stem rust fungus Puccinia graminis f. sp. tritici is limited in winter wheat (Triticum aestivum L.) germplasm adapted to the Great Plains of the United States. Our objective was to generate regionally adapted hard winter wheat germplasm with combinations of adult plant resistance genes that are expected to provide durable resistance. KS14U6380R5 (Reg. no. GP‐1043, PI 689115), KS16U6380R10 (Reg. no. GP‐1044, PI 689116), and KS16U6380R11 (Reg. no. GP‐1045, PI 689117) were derived from backcrosses of the hard white winter wheat germplasm KS05HW14 to the stem rust‐resistant Kenyan spring wheat cultivar ‘Kingbird’. KS14U6380R5, KS16U6380R11, and KS16U6380R10 were developed by pedigree selection and were initially evaluated as U6380‐11‐2R‐0A, U6380‐210‐2R‐0A, and U6380‐148‐4R‐2T, respectively. The germplasms were developed by the USDA‐ARS and jointly released with the Kansas State University Agricultural Experiment Station. These germplasms pro...
We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing comple... more We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complementary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphisms (AFLPs). We used 34 pairs of two-base selective AFLP primers and identified 1048 polymorphic markers that mapped to 468 unique loci on nine linkage groups. The total map length is ~1300 cM with an average interval of 2.8 map units between loci. Three of the nine linkage groups contain regions in which there are high levels of segregation distortion. Selection for the nitrate-utilizing recombinant progeny can explain two of the three skewed regions. Two linkage groups have recombination patterns that are consistent with the presence of intercalary inversions. Loci governing trichothecene toxin amount and type (deoxynivalenol or nivalenol) map on linkage groups IV and ...
Because of differences in life histories between Puccinia triticina, a highly specialized, polycy... more Because of differences in life histories between Puccinia triticina, a highly specialized, polycyclic, windborne pathogen with a shallow dispersal gradient, and Pyrenophora tritici-repentis, a residue-borne pathogen with a steep dispersal gradient, wheat mixtures are expected to be more effective at controlling leaf rust than tan spot. The objectives of this research were to determine the effect of two-cultivar mixtures with varying proportions and different pathogen resistance profiles on the severity of tan spot and leaf rust, to evaluate yield of the mixtures in the presence or absence of disease, and to directly compare the relative effectiveness of cultivar mixing for tan spot versus leaf rust. In a field experiment at two sites in Kansas over two growing seasons, winter wheat cvs. Jagger and 2145, which have differential resistance reactions to leaf rust and tan spot, each were planted in proportions of 0.25, 0.50, 0.75, and 1.00. Plots were inoculated with each pathogen alone...
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe... more Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for ...
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that cons... more Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly ...
Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype st... more Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. Wi...
Stem rust (caused by f. sp. Erikss. & E. Henn.), is a major disease in wheat ( L.). However, in r... more Stem rust (caused by f. sp. Erikss. & E. Henn.), is a major disease in wheat ( 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 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD,...
Genotyping-by-sequencing (GBS) is a genetic screening method for discovering and genotyping novel... more Genotyping-by-sequencing (GBS) is a genetic screening method for discovering and genotyping novel single nucleotide polymorphisms (SNPs) in crop genomes and populations. In the current research a phenotypic and genotypic assessment of 76 durum wheat (Triticum durum Desf.) accessions of Azerbaijan origin was made using six phenotypic traits and GBS technology. After screening for leaf and stem rust resistance at the seedling stage, 16 genotypes displayed resistance to leaf rust and 14 to stem rust. Some relationships were found between resistance to leaf rust and phenotypic traits of botanical varieties. The highest Pearson’s correlation (r=0.53; p < 0.001) was noted between awn color and pubescence. The durum wheat genotypes fell into four main groups in the clustered heat map; grouping according to botanical variety. A total of 748 SNP markers were obtained for the collection. The average polymorphic information content and genetic diversity index for the entire collection were ...
With climate variation common in the U.S. Great Plains and particularly in Nebraska, wheat grower... more With climate variation common in the U.S. Great Plains and particularly in Nebraska, wheat growers prefer broadly adapted cultivars. ‘NE10589’ (Reg. no. CV‐1165, PI 675998) hard red winter wheat (Triticum aestivum L.) was developed cooperatively by the Nebraska Agricultural Experiment Station and the USDA–ARS and released in January 2015 by the developing institutions. NE10589 was released primarily as a broadly adapted semi‐dwarf cultivar for its superior performance under rainfed conditions throughout Nebraska and adjacent areas of the Great Plains. Its broad adaptation ensures that it will perform well under the typical environmental fluctuations that occur in Nebraska. NE10589 was selected from the cross ‘OK98697’/‘Jagalene’//‘Camelot’, where the pedigree of OK98697 is ‘TAM 200’/‘HBB313E’//‘2158’. The F2 to F3 generations were advanced using the bulk breeding method at the Eastern Nebraska Research and Extension Center near Mead, NE, in 2006–2007. In 2007–2008, single F3:4 head ...
f. sp.() causes wheat stem rust, a devastating fungal disease. Theresistance gene confers immunit... more f. sp.() causes wheat stem rust, a devastating fungal disease. Theresistance gene confers immunity against this pathogen's most virulent races, including Ug99. We used comparative whole-genome sequencing of chemically mutagenized and naturalisolates to identify a fungal gene namedthat is required foravirulence. Thegene encodes a secreted protein capable of interacting with Sr35 and triggering the immune response. We show that the origin ofisolates virulent onis associated with the nonfunctionalization of thegene by the insertion of a mobile element. The discovery ofprovides a new tool forsurveillance, identification of host susceptibility targets, and characterization of the molecular determinants of immunity in wheat.
Western Nebraska wheat producers and those in adjacent areas want taller wheat (Triticum aestivum... more 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 furth...
Resistance to the Ug99 group of races of the stem rust fungus Puccinia graminis f. sp. tritici is... more Resistance to the Ug99 group of races of the stem rust fungus Puccinia graminis f. sp. tritici is limited in winter wheat (Triticum aestivum L.) germplasm adapted to the Great Plains of the United States. Our objective was to generate regionally adapted hard winter wheat germplasm with combinations of adult plant resistance genes that are expected to provide durable resistance. KS14U6380R5 (Reg. no. GP‐1043, PI 689115), KS16U6380R10 (Reg. no. GP‐1044, PI 689116), and KS16U6380R11 (Reg. no. GP‐1045, PI 689117) were derived from backcrosses of the hard white winter wheat germplasm KS05HW14 to the stem rust‐resistant Kenyan spring wheat cultivar ‘Kingbird’. KS14U6380R5, KS16U6380R11, and KS16U6380R10 were developed by pedigree selection and were initially evaluated as U6380‐11‐2R‐0A, U6380‐210‐2R‐0A, and U6380‐148‐4R‐2T, respectively. The germplasms were developed by the USDA‐ARS and jointly released with the Kansas State University Agricultural Experiment Station. These germplasms pro...
We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing comple... more We constructed a genetic linkage map of Gibberella zeae (Fusarium graminearum) by crossing complementary nitrate-nonutilizing (nit) mutants of G. zeae strains R-5470 (from Japan) and Z-3639 (from Kansas). We selected 99 nitrate-utilizing (recombinant) progeny and analyzed them for amplified fragment length polymorphisms (AFLPs). We used 34 pairs of two-base selective AFLP primers and identified 1048 polymorphic markers that mapped to 468 unique loci on nine linkage groups. The total map length is ~1300 cM with an average interval of 2.8 map units between loci. Three of the nine linkage groups contain regions in which there are high levels of segregation distortion. Selection for the nitrate-utilizing recombinant progeny can explain two of the three skewed regions. Two linkage groups have recombination patterns that are consistent with the presence of intercalary inversions. Loci governing trichothecene toxin amount and type (deoxynivalenol or nivalenol) map on linkage groups IV and ...
Because of differences in life histories between Puccinia triticina, a highly specialized, polycy... more Because of differences in life histories between Puccinia triticina, a highly specialized, polycyclic, windborne pathogen with a shallow dispersal gradient, and Pyrenophora tritici-repentis, a residue-borne pathogen with a steep dispersal gradient, wheat mixtures are expected to be more effective at controlling leaf rust than tan spot. The objectives of this research were to determine the effect of two-cultivar mixtures with varying proportions and different pathogen resistance profiles on the severity of tan spot and leaf rust, to evaluate yield of the mixtures in the presence or absence of disease, and to directly compare the relative effectiveness of cultivar mixing for tan spot versus leaf rust. In a field experiment at two sites in Kansas over two growing seasons, winter wheat cvs. Jagger and 2145, which have differential resistance reactions to leaf rust and tan spot, each were planted in proportions of 0.25, 0.50, 0.75, and 1.00. Plots were inoculated with each pathogen alone...
Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe... more Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for ...
Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that cons... more Scientific communication is facilitated by a data-driven, scientifically sound taxonomy that considers the end-user's needs and established successful practice. Previously (Geiser et al. 2013; Phytopathology 103:400-408. 2013), the Fusarium community voiced near unanimous support for a concept of Fusarium that represented a clade comprising all agriculturally and clinically important Fusarium species, including the F. solani Species Complex (FSSC). Subsequently, this concept was challenged by one research group (Lombard et al. 2015 Studies in Mycology 80: 189-245) who proposed dividing Fusarium into seven genera, including the FSSC as the genus Neocosmospora, with subsequent justification based on claims that the Geiser et al. (2013) concept of Fusarium is polyphyletic (Sandoval-Denis et al. 2018; Persoonia 41:109-129). Here we test this claim, and provide a phylogeny based on exonic nucleotide sequences of 19 orthologous protein-coding genes that strongly support the monophyly ...
Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype st... more Genome-wide single nucleotide polymorphism (SNP) variation allows for the capture of haplotype structure in populations and prediction of unobserved genotypes based on inferred regions of identity-by-descent (IBD). Here we have used a first-generation wheat haplotype map created by targeted re-sequencing of low-copy genomic regions in the reference panel of 62 lines to impute marker genotypes in a diverse panel of winter wheat cultivars from the U.S. Great Plains. The IBD segments between the reference population and winter wheat cultivars were identified based on SNP genotyped using the 90K iSelect wheat array and genotyping by sequencing (GBS). A genome-wide association study and genomic prediction of resistance to stripe rust in winter wheat cultivars showed that an increase in marker density achieved by imputation improved both the power and precision of trait mapping and prediction. The majority of the most significant marker-trait associations belonged to imputed genotypes. Wi...
Stem rust (caused by f. sp. Erikss. & E. Henn.), is a major disease in wheat ( L.). However, in r... more Stem rust (caused by f. sp. Erikss. & E. Henn.), is a major disease in wheat ( 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 0.05) associated with the resistance on chromosome 2D. The chromosomal location of the significant SNPs (chromosome 2D) matched the location of gene which was expected in these genotypes based on pedigree information. A highly significant linkage disequilibrium (LD,...
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Papers by Robert Bowden