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Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise.

Walia H, Wilson C, Condamine P, Ismail AM, Xu J, Cui X, Close TJ - BMC Genomics (2007)

Bottom Line: Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe.The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks.Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA. hwalia@ucdavis.edu

ABSTRACT

Background: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference.

Results: The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes.

Conclusion: The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.

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Related in: MedlinePlus

Salinity stress responsive genes in Maythorpe and Golden Promise. A. Number of probe sets up- and down-regulated in root (horizontal lines) and shoot tissue (dots) of the two genotypes. B. Venn diagram stating the overlap between the up- and down-regulated probe sets in Maythorpe (MT) and Golden Promise (GP). The overlap between the two genotypes is shaded with dots. The total number of probe sets responding in each the genotypes is indicated in brackets ().
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Figure 5: Salinity stress responsive genes in Maythorpe and Golden Promise. A. Number of probe sets up- and down-regulated in root (horizontal lines) and shoot tissue (dots) of the two genotypes. B. Venn diagram stating the overlap between the up- and down-regulated probe sets in Maythorpe (MT) and Golden Promise (GP). The overlap between the two genotypes is shaded with dots. The total number of probe sets responding in each the genotypes is indicated in brackets ().

Mentions: How different are the salinity stress responses of two genotypes which are genetically very similar but differ in salt-tolerance? How do the transcriptional responses of roots compare to those of shoot under salinity stress for a given genotype? To address these questions, the shoot and root samples from control and stressed conditions at 25-day time point from Golden Promise and Maythorpe were compared. Differential expression analysis was performed using SAM and the false discovery rate (FDR) was controlled to be below 15%. Lists of differentially expressed genes in response to salinity stress observed in Golden Promise and Maythorpe are provided as additional files (7 to 14). The number of probe sets responding significantly to salinity treatment for each of the genotype and tissue combinations is shown in Figure 5A. The results show that a higher number of genes are salt stress regulated in the roots compared to the shoot tissue in both genotypes. Additionally, roots in both genotypes responded by down-regulation of more genes than by up-regulation. The salinity stress response of Golden Promise is significantly different compared to Maythorpe (Figure 5B). This difference is more apparent in the root comparisons.


Array-based genotyping and expression analysis of barley cv. Maythorpe and Golden Promise.

Walia H, Wilson C, Condamine P, Ismail AM, Xu J, Cui X, Close TJ - BMC Genomics (2007)

Salinity stress responsive genes in Maythorpe and Golden Promise. A. Number of probe sets up- and down-regulated in root (horizontal lines) and shoot tissue (dots) of the two genotypes. B. Venn diagram stating the overlap between the up- and down-regulated probe sets in Maythorpe (MT) and Golden Promise (GP). The overlap between the two genotypes is shaded with dots. The total number of probe sets responding in each the genotypes is indicated in brackets ().
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1851953&req=5

Figure 5: Salinity stress responsive genes in Maythorpe and Golden Promise. A. Number of probe sets up- and down-regulated in root (horizontal lines) and shoot tissue (dots) of the two genotypes. B. Venn diagram stating the overlap between the up- and down-regulated probe sets in Maythorpe (MT) and Golden Promise (GP). The overlap between the two genotypes is shaded with dots. The total number of probe sets responding in each the genotypes is indicated in brackets ().
Mentions: How different are the salinity stress responses of two genotypes which are genetically very similar but differ in salt-tolerance? How do the transcriptional responses of roots compare to those of shoot under salinity stress for a given genotype? To address these questions, the shoot and root samples from control and stressed conditions at 25-day time point from Golden Promise and Maythorpe were compared. Differential expression analysis was performed using SAM and the false discovery rate (FDR) was controlled to be below 15%. Lists of differentially expressed genes in response to salinity stress observed in Golden Promise and Maythorpe are provided as additional files (7 to 14). The number of probe sets responding significantly to salinity treatment for each of the genotype and tissue combinations is shown in Figure 5A. The results show that a higher number of genes are salt stress regulated in the roots compared to the shoot tissue in both genotypes. Additionally, roots in both genotypes responded by down-regulation of more genes than by up-regulation. The salinity stress response of Golden Promise is significantly different compared to Maythorpe (Figure 5B). This difference is more apparent in the root comparisons.

Bottom Line: Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe.The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks.Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Botany and Plant Sciences, University of California, Riverside, CA, USA. hwalia@ucdavis.edu

ABSTRACT

Background: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference.

Results: The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes.

Conclusion: The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.

Show MeSH
Related in: MedlinePlus