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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.

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Distribution of d/a values for 70-mer array differentially expressed genes. Distributions of d/a (type I) ratios for differentially expressed genes based on the 70-mer oligonucleotide microarray data. (A) The d/a distributions for all differentially expressed genes. The distributions of the four hybrids are very similar to one another and peak at approximately zero, as was observed in Affymetrix microarray data. (B) The d/a distributions for the subset of differentially expressed genes that are also represented with features on the Affymetrix platform. The distributions are similar to those in (A). In both (A) and (B), the proportion of DE genes with d/a values above 3.0 or below -3.0 are all plotted as a single data point. The proportion of d/a values above 3.0 and below -3.0 for hybrid B84 × B73 plotted beyond the range of the displays and are not shown.
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Figure 7: Distribution of d/a values for 70-mer array differentially expressed genes. Distributions of d/a (type I) ratios for differentially expressed genes based on the 70-mer oligonucleotide microarray data. (A) The d/a distributions for all differentially expressed genes. The distributions of the four hybrids are very similar to one another and peak at approximately zero, as was observed in Affymetrix microarray data. (B) The d/a distributions for the subset of differentially expressed genes that are also represented with features on the Affymetrix platform. The distributions are similar to those in (A). In both (A) and (B), the proportion of DE genes with d/a values above 3.0 or below -3.0 are all plotted as a single data point. The proportion of d/a values above 3.0 and below -3.0 for hybrid B84 × B73 plotted beyond the range of the displays and are not shown.

Mentions: We also identified DE genes and calculated d/a type I values using the 70-mer oligonucleotide microarray data (see Methods for details on statistical analyses). The distribution of the d/a plots from 70-mer oligonucleotide microarray data are very similar to the plots generated from the Affymetrix data (Figure 7A). The d/a type I distribution for all four hybrids are similarly shaped, with each centered near zero (Figure 7A). However, the 70-mer oligonucleotide microarray d/a plots indicated that a substantial proportion of genes have hybrid expression levels outside of the parental range. This is evidenced by the fact that many of the genes exhibit d/a type I values greater than 1.0 or less than -1.0 (Figure 7A). In total, 20.6% of the DE patterns exhibited d/a values outside the parental range in the 70-mer oligonucleotide microarray data. By comparison, the Affymetrix d/a distributions were nearly flat outside of these values and only 1.3% of the DE patterns exhibited d/a values outside the parental range (Figure 6).


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)

Distribution of d/a values for 70-mer array differentially expressed genes. Distributions of d/a (type I) ratios for differentially expressed genes based on the 70-mer oligonucleotide microarray data. (A) The d/a distributions for all differentially expressed genes. The distributions of the four hybrids are very similar to one another and peak at approximately zero, as was observed in Affymetrix microarray data. (B) The d/a distributions for the subset of differentially expressed genes that are also represented with features on the Affymetrix platform. The distributions are similar to those in (A). In both (A) and (B), the proportion of DE genes with d/a values above 3.0 or below -3.0 are all plotted as a single data point. The proportion of d/a values above 3.0 and below -3.0 for hybrid B84 × B73 plotted beyond the range of the displays and are not shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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Figure 7: Distribution of d/a values for 70-mer array differentially expressed genes. Distributions of d/a (type I) ratios for differentially expressed genes based on the 70-mer oligonucleotide microarray data. (A) The d/a distributions for all differentially expressed genes. The distributions of the four hybrids are very similar to one another and peak at approximately zero, as was observed in Affymetrix microarray data. (B) The d/a distributions for the subset of differentially expressed genes that are also represented with features on the Affymetrix platform. The distributions are similar to those in (A). In both (A) and (B), the proportion of DE genes with d/a values above 3.0 or below -3.0 are all plotted as a single data point. The proportion of d/a values above 3.0 and below -3.0 for hybrid B84 × B73 plotted beyond the range of the displays and are not shown.
Mentions: We also identified DE genes and calculated d/a type I values using the 70-mer oligonucleotide microarray data (see Methods for details on statistical analyses). The distribution of the d/a plots from 70-mer oligonucleotide microarray data are very similar to the plots generated from the Affymetrix data (Figure 7A). The d/a type I distribution for all four hybrids are similarly shaped, with each centered near zero (Figure 7A). However, the 70-mer oligonucleotide microarray d/a plots indicated that a substantial proportion of genes have hybrid expression levels outside of the parental range. This is evidenced by the fact that many of the genes exhibit d/a type I values greater than 1.0 or less than -1.0 (Figure 7A). In total, 20.6% of the DE patterns exhibited d/a values outside the parental range in the 70-mer oligonucleotide microarray data. By comparison, the Affymetrix d/a distributions were nearly flat outside of these values and only 1.3% of the DE patterns exhibited d/a values outside the parental range (Figure 6).

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