Limits...
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.

Show MeSH

Related in: MedlinePlus

Differentially expressed genes and 5H wheat-barley addition line. Some of the differentially expressed genes were checked for map position on chromosome 5H of barley (Ari-e locus is on 5H). Wheat background genotype used is Chinese Spring (CS), the barley genotype Betzes, and the addition line is 5H. None of the genes identified by array analysis (LEA, CCT motif protein, HUA1, Replication protein A, catalase1, and ARF2) mapped to 5H. A gene which maps to 5H (e.g. Timing of CAB expression 1, TOC1) is expected to have a stronger band in 5H relative to CS. Three genes CCT, catalase 1 and ARF2 have different alleles in Maythorpe (MT) and Golden Promise (GP).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1851953&req=5

Figure 3: Differentially expressed genes and 5H wheat-barley addition line. Some of the differentially expressed genes were checked for map position on chromosome 5H of barley (Ari-e locus is on 5H). Wheat background genotype used is Chinese Spring (CS), the barley genotype Betzes, and the addition line is 5H. None of the genes identified by array analysis (LEA, CCT motif protein, HUA1, Replication protein A, catalase1, and ARF2) mapped to 5H. A gene which maps to 5H (e.g. Timing of CAB expression 1, TOC1) is expected to have a stronger band in 5H relative to CS. Three genes CCT, catalase 1 and ARF2 have different alleles in Maythorpe (MT) and Golden Promise (GP).

Mentions: Since the GPert mutation in Golden Promise was previously mapped to barley chromosome 5H as an allele of the ari-e locus [7], we initially used wheat-barley addition line for 5H [26] to determine if any of the regulated genes identified from array analysis map to 5H. Six genes encoding LEA protein, CCT motif family protein, Hua1, replication protein A (RepA), Catalase1 and auxin response factor (Arf2) from Table 3 were selected. Selection of these genes was based on their identification from two or more expression-based genotypic comparisons involving 10-day and 25-day Golden Promise-Maythorpe comparisons and the Golden Promise-Morex comparisons. The 5H addition line consists of disomic 5H from Betzes barley in the Chinese Spring hexaploid wheat background (Figure 3). None of these genes mapped on 5H, consistent with SFP and SNP analysis. Furthermore, size polymorphisms in the amplicons for CCT motif protein, and catalase1 and a missing band for Maythorpe (presence/absence polymorphism) in the case of Arf2 were detected. These amplicon size polymorphisms indicated that these three genes were not only differentially expressed but were in different allelic forms in the two genotypes. The difference in expression for CCT motif protein and catalase1 was validated with semi-quantitative RT-PCR (Figure 4).


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)

Differentially expressed genes and 5H wheat-barley addition line. Some of the differentially expressed genes were checked for map position on chromosome 5H of barley (Ari-e locus is on 5H). Wheat background genotype used is Chinese Spring (CS), the barley genotype Betzes, and the addition line is 5H. None of the genes identified by array analysis (LEA, CCT motif protein, HUA1, Replication protein A, catalase1, and ARF2) mapped to 5H. A gene which maps to 5H (e.g. Timing of CAB expression 1, TOC1) is expected to have a stronger band in 5H relative to CS. Three genes CCT, catalase 1 and ARF2 have different alleles in Maythorpe (MT) and Golden Promise (GP).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 3: Differentially expressed genes and 5H wheat-barley addition line. Some of the differentially expressed genes were checked for map position on chromosome 5H of barley (Ari-e locus is on 5H). Wheat background genotype used is Chinese Spring (CS), the barley genotype Betzes, and the addition line is 5H. None of the genes identified by array analysis (LEA, CCT motif protein, HUA1, Replication protein A, catalase1, and ARF2) mapped to 5H. A gene which maps to 5H (e.g. Timing of CAB expression 1, TOC1) is expected to have a stronger band in 5H relative to CS. Three genes CCT, catalase 1 and ARF2 have different alleles in Maythorpe (MT) and Golden Promise (GP).
Mentions: Since the GPert mutation in Golden Promise was previously mapped to barley chromosome 5H as an allele of the ari-e locus [7], we initially used wheat-barley addition line for 5H [26] to determine if any of the regulated genes identified from array analysis map to 5H. Six genes encoding LEA protein, CCT motif family protein, Hua1, replication protein A (RepA), Catalase1 and auxin response factor (Arf2) from Table 3 were selected. Selection of these genes was based on their identification from two or more expression-based genotypic comparisons involving 10-day and 25-day Golden Promise-Maythorpe comparisons and the Golden Promise-Morex comparisons. The 5H addition line consists of disomic 5H from Betzes barley in the Chinese Spring hexaploid wheat background (Figure 3). None of these genes mapped on 5H, consistent with SFP and SNP analysis. Furthermore, size polymorphisms in the amplicons for CCT motif protein, and catalase1 and a missing band for Maythorpe (presence/absence polymorphism) in the case of Arf2 were detected. These amplicon size polymorphisms indicated that these three genes were not only differentially expressed but were in different allelic forms in the two genotypes. The difference in expression for CCT motif protein and catalase1 was validated with semi-quantitative RT-PCR (Figure 4).

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