Limits...
Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.

Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM - BMC Plant Biol. (2008)

Bottom Line: We have found that maize inbred genetic diversity is correlated with transcriptional variation.These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents.The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Plant and Microbial Genomics, Department of Plant Biology, University of Minnesota, Saint Paul MN 55108, USA. stup0004@umn.edu

ABSTRACT

Background: Heterosis is the superior performance of F1 hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.

Results: We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and approximately 25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, approximately 80% exhibited hybrid expression levels between the parental levels, approximately 20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.

Conclusion: We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.

Show MeSH

Related in: MedlinePlus

Validation of differential expression using MassArray and 70-mer platforms. The magnitude of differential expression between inbred lines based on the Affymetrix data was compared to the magnitude of differential expression detected using the MassArray platform and 70-mer microarray platform. The subset of the genes identified as differentially expressed on the Affymetrix platform (FDR < 0.05, and additional quality control filters; see Methods) was used for these analyses. The color coding of the data points indicates the inbred genotype comparison. (A) The same inbred RNA samples used for Affymetrix microarray analyses were mixed in a pairwise 1:1 ratio and subjected to MassArray relative allelic quantification [25]. The correlation between the MassArray proportions and the proportions calculated from the Affymetrix dataset (inbred 1 signal divided by the sum of the two inbred signals) are shown. Each spot represents the proportion of one allele per inbred-inbred comparison. The B73 and Mo17 sequence SNPs were used to design the assays, thus this comparison is most highly represented in this analysis. (B) Many genes that were determined to be differentially expressed in the Affymetrix dataset were also present on the 70-mer microarray platform. The correlation of the inbred expression fold-differences on the 70-mer oligonucleotide microarray and the Affymetrix microarray are shown. Each spot represents the fold-differences of one gene per inbred-inbred comparison. The 70-mer microarray data validated the directionality of the Affymetrix microarray patterns in 84–91% of the differentially expressed profiles (see main text).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2365949&req=5

Figure 5: Validation of differential expression using MassArray and 70-mer platforms. The magnitude of differential expression between inbred lines based on the Affymetrix data was compared to the magnitude of differential expression detected using the MassArray platform and 70-mer microarray platform. The subset of the genes identified as differentially expressed on the Affymetrix platform (FDR < 0.05, and additional quality control filters; see Methods) was used for these analyses. The color coding of the data points indicates the inbred genotype comparison. (A) The same inbred RNA samples used for Affymetrix microarray analyses were mixed in a pairwise 1:1 ratio and subjected to MassArray relative allelic quantification [25]. The correlation between the MassArray proportions and the proportions calculated from the Affymetrix dataset (inbred 1 signal divided by the sum of the two inbred signals) are shown. Each spot represents the proportion of one allele per inbred-inbred comparison. The B73 and Mo17 sequence SNPs were used to design the assays, thus this comparison is most highly represented in this analysis. (B) Many genes that were determined to be differentially expressed in the Affymetrix dataset were also present on the 70-mer microarray platform. The correlation of the inbred expression fold-differences on the 70-mer oligonucleotide microarray and the Affymetrix microarray are shown. Each spot represents the fold-differences of one gene per inbred-inbred comparison. The 70-mer microarray data validated the directionality of the Affymetrix microarray patterns in 84–91% of the differentially expressed profiles (see main text).

Mentions: The use of microarray expression profiling for intraspecific comparisons can be complicated by the presence of sequence polymorphisms within different inbred lines [25]. We assessed the frequency of false-positive DE genes in our Affymetrix dataset by validating the microarray data using two independent methodologies. First, the Sequenom MassArray platform was used to validate calls of differential expression between different inbred lines. We had previously used the MassArray platform to measure allele-specific expression levels for a set of ~300 genes using the same RNA samples as were used in the Affymetrix analyses [26]. The MassArray platform can detect the relative allelic proportions for a given gene in a mix of parental RNAs. The relative proportion detected for each allele can be compared with the proportion predicted based on the Affymetrix data, as was demonstrated in Stupar and Springer [17]. Fifty-six genes that were DE in the Affymetrix data were subjected to MassArray validation (this includes six genes that were DE in two different inbred-hybrid groups, resulting in validation assays for 62 DE profiles). The correlation between the Affymetrix and MassArray data was strong, with 58 of the 62 examples showing similar directionality of biased expression in both platforms (Figure 5A). A statistical analysis indicated that 74% (46/62) of the genes exhibit significant differential expression in the MassArray dataset. Second, we utilized a maize 70-mer oligonucleotide microarray platform [27] to validate the DE genes observed in the Affymetrix dataset. The same sets of RNA samples were labelled and hybridized to the 70-mer oligonucleotide microarray containing ~43,000 features. We identified a set of 13,874 features on this platform that are expected to detect the same transcripts as the Affymetrix platform. For all Affymetrix DE genes that are present on the 70-mer oligonucleotide microarray we compared the log2 expression differences between parental inbred lines on both platforms (Figure 5B). Pearson R values indicated significant correlations (p < 0.0001) for all of the comparisons (R = 0.697 for B84 versus B73; R = 0.679 for B37 versus B73; R = 0.720 for Oh43 versus B73; R = 0.750 for Oh43 versus Mo17). The 70-mer oligonucleotide microarray platform confirmed the directionality of the expression differences between parental inbred genotypes for the vast majority of the genes identified by Affymetrix (Figure 5B; ~91% for B84 versus B73; ~84% for B37 versus B73; ~84% for Oh43 versus B73; ~91% for Oh43 versus Mo17). While there are some examples in which differential expression is only detected using one of the platforms, the majority of genes exhibited similar differential expression in both microarray platforms. Both the Sequenom MassArray and 70-mer oligonucleotide microarray analyses indicate that the majority of the DE profiles identified using the Affymetrix microarrays were valid.


Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis.

Stupar RM, Gardiner JM, Oldre AG, Haun WJ, Chandler VL, Springer NM - BMC Plant Biol. (2008)

Validation of differential expression using MassArray and 70-mer platforms. The magnitude of differential expression between inbred lines based on the Affymetrix data was compared to the magnitude of differential expression detected using the MassArray platform and 70-mer microarray platform. The subset of the genes identified as differentially expressed on the Affymetrix platform (FDR < 0.05, and additional quality control filters; see Methods) was used for these analyses. The color coding of the data points indicates the inbred genotype comparison. (A) The same inbred RNA samples used for Affymetrix microarray analyses were mixed in a pairwise 1:1 ratio and subjected to MassArray relative allelic quantification [25]. The correlation between the MassArray proportions and the proportions calculated from the Affymetrix dataset (inbred 1 signal divided by the sum of the two inbred signals) are shown. Each spot represents the proportion of one allele per inbred-inbred comparison. The B73 and Mo17 sequence SNPs were used to design the assays, thus this comparison is most highly represented in this analysis. (B) Many genes that were determined to be differentially expressed in the Affymetrix dataset were also present on the 70-mer microarray platform. The correlation of the inbred expression fold-differences on the 70-mer oligonucleotide microarray and the Affymetrix microarray are shown. Each spot represents the fold-differences of one gene per inbred-inbred comparison. The 70-mer microarray data validated the directionality of the Affymetrix microarray patterns in 84–91% of the differentially expressed profiles (see main text).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2365949&req=5

Figure 5: Validation of differential expression using MassArray and 70-mer platforms. The magnitude of differential expression between inbred lines based on the Affymetrix data was compared to the magnitude of differential expression detected using the MassArray platform and 70-mer microarray platform. The subset of the genes identified as differentially expressed on the Affymetrix platform (FDR < 0.05, and additional quality control filters; see Methods) was used for these analyses. The color coding of the data points indicates the inbred genotype comparison. (A) The same inbred RNA samples used for Affymetrix microarray analyses were mixed in a pairwise 1:1 ratio and subjected to MassArray relative allelic quantification [25]. The correlation between the MassArray proportions and the proportions calculated from the Affymetrix dataset (inbred 1 signal divided by the sum of the two inbred signals) are shown. Each spot represents the proportion of one allele per inbred-inbred comparison. The B73 and Mo17 sequence SNPs were used to design the assays, thus this comparison is most highly represented in this analysis. (B) Many genes that were determined to be differentially expressed in the Affymetrix dataset were also present on the 70-mer microarray platform. The correlation of the inbred expression fold-differences on the 70-mer oligonucleotide microarray and the Affymetrix microarray are shown. Each spot represents the fold-differences of one gene per inbred-inbred comparison. The 70-mer microarray data validated the directionality of the Affymetrix microarray patterns in 84–91% of the differentially expressed profiles (see main text).
Mentions: The use of microarray expression profiling for intraspecific comparisons can be complicated by the presence of sequence polymorphisms within different inbred lines [25]. We assessed the frequency of false-positive DE genes in our Affymetrix dataset by validating the microarray data using two independent methodologies. First, the Sequenom MassArray platform was used to validate calls of differential expression between different inbred lines. We had previously used the MassArray platform to measure allele-specific expression levels for a set of ~300 genes using the same RNA samples as were used in the Affymetrix analyses [26]. The MassArray platform can detect the relative allelic proportions for a given gene in a mix of parental RNAs. The relative proportion detected for each allele can be compared with the proportion predicted based on the Affymetrix data, as was demonstrated in Stupar and Springer [17]. Fifty-six genes that were DE in the Affymetrix data were subjected to MassArray validation (this includes six genes that were DE in two different inbred-hybrid groups, resulting in validation assays for 62 DE profiles). The correlation between the Affymetrix and MassArray data was strong, with 58 of the 62 examples showing similar directionality of biased expression in both platforms (Figure 5A). A statistical analysis indicated that 74% (46/62) of the genes exhibit significant differential expression in the MassArray dataset. Second, we utilized a maize 70-mer oligonucleotide microarray platform [27] to validate the DE genes observed in the Affymetrix dataset. The same sets of RNA samples were labelled and hybridized to the 70-mer oligonucleotide microarray containing ~43,000 features. We identified a set of 13,874 features on this platform that are expected to detect the same transcripts as the Affymetrix platform. For all Affymetrix DE genes that are present on the 70-mer oligonucleotide microarray we compared the log2 expression differences between parental inbred lines on both platforms (Figure 5B). Pearson R values indicated significant correlations (p < 0.0001) for all of the comparisons (R = 0.697 for B84 versus B73; R = 0.679 for B37 versus B73; R = 0.720 for Oh43 versus B73; R = 0.750 for Oh43 versus Mo17). The 70-mer oligonucleotide microarray platform confirmed the directionality of the expression differences between parental inbred genotypes for the vast majority of the genes identified by Affymetrix (Figure 5B; ~91% for B84 versus B73; ~84% for B37 versus B73; ~84% for Oh43 versus B73; ~91% for Oh43 versus Mo17). While there are some examples in which differential expression is only detected using one of the platforms, the majority of genes exhibited similar differential expression in both microarray platforms. Both the Sequenom MassArray and 70-mer oligonucleotide microarray analyses indicate that the majority of the DE profiles identified using the Affymetrix microarrays were valid.

Bottom Line: We have found that maize inbred genetic diversity is correlated with transcriptional variation.These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents.The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center for Plant and Microbial Genomics, Department of Plant Biology, University of Minnesota, Saint Paul MN 55108, USA. stup0004@umn.edu

ABSTRACT

Background: Heterosis is the superior performance of F1 hybrid progeny relative to the parental phenotypes. Maize exhibits heterosis for a wide range of traits, however the magnitude of heterosis is highly variable depending on the choice of parents and the trait(s) measured. We have used expression profiling to determine whether the level, or types, of non-additive gene expression vary in maize hybrids with different levels of genetic diversity or heterosis.

Results: We observed that the distributions of better parent heterosis among a series of 25 maize hybrids generally do not exhibit significant correlations between different traits. Expression profiling analyses for six of these hybrids, chosen to represent diversity in genotypes and heterosis responses, revealed a correlation between genetic diversity and transcriptional variation. The majority of differentially expressed genes in each of the six different hybrids exhibited additive expression patterns, and approximately 25% exhibited statistically significant non-additive expression profiles. Among the non-additive profiles, approximately 80% exhibited hybrid expression levels between the parental levels, approximately 20% exhibited hybrid expression levels at the parental levels and ~1% exhibited hybrid levels outside the parental range.

Conclusion: We have found that maize inbred genetic diversity is correlated with transcriptional variation. However, sampling of seedling tissues indicated that the frequencies of additive and non-additive expression patterns are very similar across a range of hybrid lines. These findings suggest that heterosis is probably not a consequence of higher levels of additive or non-additive expression, but may be related to transcriptional variation between parents. The lack of correlation between better parent heterosis levels for different traits suggests that transcriptional diversity at specific sets of genes may influence heterosis for different traits.

Show MeSH
Related in: MedlinePlus