Skip to main content

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Research Abstract
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.
Research Authors
Amira M. I. Mourad1, Ahmed Sallam, Vikas Belamkar, Stephen Wegulo, Robert Bowden, Yue Jin, Ezzat Mahdy, Bahy Bakheit, Atif A. El-Wafaa, Jesse Poland and Peter S. Baenziger
Research Department
Research Journal
Frontiers in Plant Science
Research Pages
pp. 1-11
Research Publisher
Frontiers
Research Rank
1
Research Vol
Vol. 9 - No. 380
Research Website
https://www.frontiersin.org/articles/10.3389/fpls.2018.00380/full
Research Year
2018

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Research Abstract
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.
Research Authors
Amira M. I. Mourad1, Ahmed Sallam, Vikas Belamkar, Stephen Wegulo, Robert Bowden, Yue Jin, Ezzat Mahdy, Bahy Bakheit, Atif A. El-Wafaa, Jesse Poland and Peter S. Baenziger
Research Department
Research Journal
Frontiers in Plant Science
Research Pages
pp. 1-11
Research Publisher
Frontiers
Research Rank
1
Research Vol
Vol. 9 - No. 380
Research Website
https://www.frontiersin.org/articles/10.3389/fpls.2018.00380/full
Research Year
2018

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Research Abstract
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.
Research Authors
Amira M. I. Mourad1, Ahmed Sallam, Vikas Belamkar, Stephen Wegulo, Robert Bowden, Yue Jin, Ezzat Mahdy, Bahy Bakheit, Atif A. El-Wafaa, Jesse Poland and Peter S. Baenziger
Research Department
Research Journal
Frontiers in Plant Science
Research Member
Research Pages
pp. 1-11
Research Publisher
Frontiers
Research Rank
1
Research Vol
Vol. 9 - No. 380
Research Website
https://www.frontiersin.org/articles/10.3389/fpls.2018.00380/full
Research Year
2018

Genome-Wide Association Study for Identification and Validation of Novel SNP Markers for Sr6 Stem Rust Resistance Gene in Bread Wheat

Research Abstract
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.
Research Authors
Amira M. I. Mourad1, Ahmed Sallam, Vikas Belamkar, Stephen Wegulo, Robert Bowden, Yue Jin, Ezzat Mahdy, Bahy Bakheit, Atif A. El-Wafaa, Jesse Poland and Peter S. Baenziger
Research Department
Research Journal
Frontiers in Plant Science
Research Member
Research Pages
pp. 1-11
Research Publisher
Frontiers
Research Rank
1
Research Vol
Vol. 9 - No. 380
Research Website
https://www.frontiersin.org/articles/10.3389/fpls.2018.00380/full
Research Year
2018

Hepato-morpholoy and biochemical studies on the liver of albino rats after exposure to glyphosate-Roundup®

Research Abstract
Background: The object of this work was to evaluate of the hepatic effects of the herbicides glyphosate-Roundup® by different doses in both sexes of albino rats. Methods: Forty animals divided into four groups with ten animals for each (both sexes) were treated orally with vehicle (controls) and 25, 50, and 100 mg/kg bwt of glyphosate-Roundup® (treated groups) for 15 days daily. Results: The most conspicuous changes occurred on the liver treated groups due to glyphosate toxicity were the increase of enzymes activities of ALT and AST, cellular infiltration, many signs of nucleus degeneration, focal necrosis, rarified cytoplasm, disorganization of cellular organelles, and deposition of lipid droplets. The increase in the amount of collagenous fibers and the number of the mast cell were also observed. Conclusion: Our results indicated that the administration of glyphosate-Roundup® in different doses may cause adverse effects on the histopathological, ultrastructure, and biochemical alternations on the liver of the albino rats.
Research Authors
Shaimaa M. M. Saleh , Tasneem A. Elghareeb , Mohamed A. I. Ahmed , Ibrahim A. Mohamed , Hosam A. Ezz El-Din
Research Department
Research Journal
The Journal of Basic and Applied Zoology
Research Pages
1-11
Research Publisher
Springer
Research Rank
1
Research Vol
79(48)
Research Website
https://basicandappliedzoology.springeropen.com/articles/10.1186/s41936-018-0060-4
Research Year
2018

Hepato-morpholoy and biochemical studies on the liver of albino rats after exposure to glyphosate-Roundup®

Research Abstract
Background: The object of this work was to evaluate of the hepatic effects of the herbicides glyphosate-Roundup® by different doses in both sexes of albino rats. Methods: Forty animals divided into four groups with ten animals for each (both sexes) were treated orally with vehicle (controls) and 25, 50, and 100 mg/kg bwt of glyphosate-Roundup® (treated groups) for 15 days daily. Results: The most conspicuous changes occurred on the liver treated groups due to glyphosate toxicity were the increase of enzymes activities of ALT and AST, cellular infiltration, many signs of nucleus degeneration, focal necrosis, rarified cytoplasm, disorganization of cellular organelles, and deposition of lipid droplets. The increase in the amount of collagenous fibers and the number of the mast cell were also observed. Conclusion: Our results indicated that the administration of glyphosate-Roundup® in different doses may cause adverse effects on the histopathological, ultrastructure, and biochemical alternations on the liver of the albino rats.
Research Authors
Shaimaa M. M. Saleh , Tasneem A. Elghareeb , Mohamed A. I. Ahmed , Ibrahim A. Mohamed , Hosam A. Ezz El-Din
Research Department
Research Journal
The Journal of Basic and Applied Zoology
Research Member
Research Pages
1-11
Research Publisher
Springer
Research Rank
1
Research Vol
79(48)
Research Website
https://basicandappliedzoology.springeropen.com/articles/10.1186/s41936-018-0060-4
Research Year
2018

Hepato-morpholoy and biochemical studies on the liver of albino rats after exposure to glyphosate-Roundup®

Research Abstract
Background: The object of this work was to evaluate of the hepatic effects of the herbicides glyphosate-Roundup® by different doses in both sexes of albino rats. Methods: Forty animals divided into four groups with ten animals for each (both sexes) were treated orally with vehicle (controls) and 25, 50, and 100 mg/kg bwt of glyphosate-Roundup® (treated groups) for 15 days daily. Results: The most conspicuous changes occurred on the liver treated groups due to glyphosate toxicity were the increase of enzymes activities of ALT and AST, cellular infiltration, many signs of nucleus degeneration, focal necrosis, rarified cytoplasm, disorganization of cellular organelles, and deposition of lipid droplets. The increase in the amount of collagenous fibers and the number of the mast cell were also observed. Conclusion: Our results indicated that the administration of glyphosate-Roundup® in different doses may cause adverse effects on the histopathological, ultrastructure, and biochemical alternations on the liver of the albino rats.
Research Authors
Shaimaa M. M. Saleh , Tasneem A. Elghareeb , Mohamed A. I. Ahmed , Ibrahim A. Mohamed , Hosam A. Ezz El-Din
Research Department
Research Journal
The Journal of Basic and Applied Zoology
Research Member
Research Pages
1-11
Research Publisher
Springer
Research Rank
1
Research Vol
79(48)
Research Website
https://basicandappliedzoology.springeropen.com/articles/10.1186/s41936-018-0060-4
Research Year
2018

Hepato-morpholoy and biochemical studies on the liver of albino rats after exposure to glyphosate-Roundup®

Research Abstract
Background: The object of this work was to evaluate of the hepatic effects of the herbicides glyphosate-Roundup® by different doses in both sexes of albino rats. Methods: Forty animals divided into four groups with ten animals for each (both sexes) were treated orally with vehicle (controls) and 25, 50, and 100 mg/kg bwt of glyphosate-Roundup® (treated groups) for 15 days daily. Results: The most conspicuous changes occurred on the liver treated groups due to glyphosate toxicity were the increase of enzymes activities of ALT and AST, cellular infiltration, many signs of nucleus degeneration, focal necrosis, rarified cytoplasm, disorganization of cellular organelles, and deposition of lipid droplets. The increase in the amount of collagenous fibers and the number of the mast cell were also observed. Conclusion: Our results indicated that the administration of glyphosate-Roundup® in different doses may cause adverse effects on the histopathological, ultrastructure, and biochemical alternations on the liver of the albino rats.
Research Authors
Shaimaa M. M. Saleh , Tasneem A. Elghareeb , Mohamed A. I. Ahmed , Ibrahim A. Mohamed , Hosam A. Ezz El-Din
Research Journal
The Journal of Basic and Applied Zoology
Research Pages
1-11
Research Publisher
Springer
Research Rank
1
Research Vol
79(48)
Research Website
https://basicandappliedzoology.springeropen.com/articles/10.1186/s41936-018-0060-4
Research Year
2018

Optimizing Micropropagation Protocol for Rosa hybrida cv. Eiffel Tower with Improved in vitro Rooting Ability

Research Abstract
IN vitro propagation techniques were studied to establish a protocol for rapid and mass production of Rosa spp. cv. Eiffel Tower, an important and endangered cultivar. Several experiments were conducted through a two-stage procedure: multiplication stage and rooting of microshoots stage. For multiplication, the best results were obtained when nodal segments were cultured on MS medium supplemented with BAP at 1mg/l and/or Kinetin at 0.5 mg/l. The highest shoots number (3.17 shoots/explant) was obtained when 0.5 mg/l BAP was added to the medium. Kinetin at 0.5 mg/l produced the highest shoot number/explant (3.67 shoots), and shoot length (3.67 cm). The interaction between BAP at 1 mg/l plus kinetin at 0.5 mg/l gave the highest shoot number/explant (4 shoots). For rooting, the best interaction effect on rooting percentage (61.00%), highest number of roots/shoot (5.12) and root length (3.33 cm) were observed when the shoots were cultured on hormone-free MS medium and pH level was adjusted to 5.5. Moreover, adjusting the medium pH to 5.5 formed roots faster in 17.67 days followed by medium with pH level 4.5 (18 days). The medium with pH at 5.5 supplemented with 50 g/l sucrose produced the highest significant value of rooting (85%) and enhanced root formation in 7.5 days. The rooted plantlets were transplanted into the potting substrate and successfully acclimatized in the laboratory then transferred to the field with a survival rate of 55%. After 6 month, the plantlets reached ~ 22 cm in length and 5.50 leaves/plant
Research Authors
Azza A. Tawfik, O.H.M. Ibrahim, E.Y. Abdul-Hafeez, Samar A.I. Ibrahim
Research Department
Research Journal
Egyptian Journal of Horticulture
Research Pages
323-335
Research Publisher
National Information and Documentation Centre (NIDOC)
Research Rank
2
Research Vol
45 (2)
Research Website
http://ejoh.journals.ekb.eg/article_17155_14d5966bb921359e38d3a2d6bed2f159.pdf
Research Year
2018

Optimizing Micropropagation Protocol for Rosa hybrida cv. Eiffel Tower with Improved in vitro Rooting Ability

Research Abstract
IN vitro propagation techniques were studied to establish a protocol for rapid and mass production of Rosa spp. cv. Eiffel Tower, an important and endangered cultivar. Several experiments were conducted through a two-stage procedure: multiplication stage and rooting of microshoots stage. For multiplication, the best results were obtained when nodal segments were cultured on MS medium supplemented with BAP at 1mg/l and/or Kinetin at 0.5 mg/l. The highest shoots number (3.17 shoots/explant) was obtained when 0.5 mg/l BAP was added to the medium. Kinetin at 0.5 mg/l produced the highest shoot number/explant (3.67 shoots), and shoot length (3.67 cm). The interaction between BAP at 1 mg/l plus kinetin at 0.5 mg/l gave the highest shoot number/explant (4 shoots). For rooting, the best interaction effect on rooting percentage (61.00%), highest number of roots/shoot (5.12) and root length (3.33 cm) were observed when the shoots were cultured on hormone-free MS medium and pH level was adjusted to 5.5. Moreover, adjusting the medium pH to 5.5 formed roots faster in 17.67 days followed by medium with pH level 4.5 (18 days). The medium with pH at 5.5 supplemented with 50 g/l sucrose produced the highest significant value of rooting (85%) and enhanced root formation in 7.5 days. The rooted plantlets were transplanted into the potting substrate and successfully acclimatized in the laboratory then transferred to the field with a survival rate of 55%. After 6 month, the plantlets reached ~ 22 cm in length and 5.50 leaves/plant
Research Authors
Azza A. Tawfik, O.H.M. Ibrahim, E.Y. Abdul-Hafeez, Samar A.I. Ibrahim
Research Department
Research Journal
Egyptian Journal of Horticulture
Research Pages
323-335
Research Publisher
National Information and Documentation Centre (NIDOC)
Research Rank
2
Research Vol
45 (2)
Research Website
http://ejoh.journals.ekb.eg/article_17155_14d5966bb921359e38d3a2d6bed2f159.pdf
Research Year
2018
Subscribe to