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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.

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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 Affymetrix differentially expressed genes. Distributions of d/a ratios for differentially expressed genes based on Affymetrix microarray data. (A) d/a type I values indicate the hybrid expression levels relative to the low-parent and high-parent levels. The distributions are very similar for the six different hybrids. Hybrid expression patterns center approximately around the mid-parent level with very flat distributions outside of the parental range. (B) d/a type II values indicate the hybrid expression levels relative to the maternal-parent and paternal-parent levels. Again, all six hybrids exhibit similar distributions peaking around mid-parent levels, indicating no maternal or paternal expression biases. (C) The distributions of d/a type II values for the subset of differentially expressed genes that exhibited non-additive hybrid expression profiles. The distributions indicate that the non-additive patterns for most genes are still within the parental range, and are oftentimes observed near the mid-parent (additive) values.
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Figure 6: Distribution of d/a values for Affymetrix differentially expressed genes. Distributions of d/a ratios for differentially expressed genes based on Affymetrix microarray data. (A) d/a type I values indicate the hybrid expression levels relative to the low-parent and high-parent levels. The distributions are very similar for the six different hybrids. Hybrid expression patterns center approximately around the mid-parent level with very flat distributions outside of the parental range. (B) d/a type II values indicate the hybrid expression levels relative to the maternal-parent and paternal-parent levels. Again, all six hybrids exhibit similar distributions peaking around mid-parent levels, indicating no maternal or paternal expression biases. (C) The distributions of d/a type II values for the subset of differentially expressed genes that exhibited non-additive hybrid expression profiles. The distributions indicate that the non-additive patterns for most genes are still within the parental range, and are oftentimes observed near the mid-parent (additive) values.

Mentions: We performed the d/a calculations in two different ways (see Methods for calculation details). The first d/a calculation (hereafter termed 'd/a type I') assesses the hybrid expression levels relative to the high parent and low parent for each gene. The second d/a calculation (hereafter termed 'd/a type II') assesses the hybrid expression levels relative to the maternal parent and paternal parent, allowing for the identification of maternal or paternal effects on gene expression in the hybrid. The distributions of the d/a values for the six different inbred-hybrid groups were strikingly similar (Figure 6A–B). The d/a type I distribution for all six hybrids is centered at approximately zero, and the distribution tails consistently flattened within the parental range (between -1.0 and 1.0) (Figure 6A). We did note that the center of the d/a type I distribution is skewed slightly towards the low parent. We suspected that the slight deviation of d/a type I values from the mid-parent levels may be caused by technical rather than biological factors. We found that genes with lower expression signals exhibited greater deviation from zero than genes with high expression signals [see Additional file 5]. The d/a type I distribution for genes with at least one genotype signal > 10000 units exhibited no deviation from zero for all six hybrids [see Additional file 5]. These findings suggest that technical factors, such as a slightly non-linear dynamic range among the lower microarray signal intensities, may be causing the slightly skewed distributions.


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 Affymetrix differentially expressed genes. Distributions of d/a ratios for differentially expressed genes based on Affymetrix microarray data. (A) d/a type I values indicate the hybrid expression levels relative to the low-parent and high-parent levels. The distributions are very similar for the six different hybrids. Hybrid expression patterns center approximately around the mid-parent level with very flat distributions outside of the parental range. (B) d/a type II values indicate the hybrid expression levels relative to the maternal-parent and paternal-parent levels. Again, all six hybrids exhibit similar distributions peaking around mid-parent levels, indicating no maternal or paternal expression biases. (C) The distributions of d/a type II values for the subset of differentially expressed genes that exhibited non-additive hybrid expression profiles. The distributions indicate that the non-additive patterns for most genes are still within the parental range, and are oftentimes observed near the mid-parent (additive) values.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 6: Distribution of d/a values for Affymetrix differentially expressed genes. Distributions of d/a ratios for differentially expressed genes based on Affymetrix microarray data. (A) d/a type I values indicate the hybrid expression levels relative to the low-parent and high-parent levels. The distributions are very similar for the six different hybrids. Hybrid expression patterns center approximately around the mid-parent level with very flat distributions outside of the parental range. (B) d/a type II values indicate the hybrid expression levels relative to the maternal-parent and paternal-parent levels. Again, all six hybrids exhibit similar distributions peaking around mid-parent levels, indicating no maternal or paternal expression biases. (C) The distributions of d/a type II values for the subset of differentially expressed genes that exhibited non-additive hybrid expression profiles. The distributions indicate that the non-additive patterns for most genes are still within the parental range, and are oftentimes observed near the mid-parent (additive) values.
Mentions: We performed the d/a calculations in two different ways (see Methods for calculation details). The first d/a calculation (hereafter termed 'd/a type I') assesses the hybrid expression levels relative to the high parent and low parent for each gene. The second d/a calculation (hereafter termed 'd/a type II') assesses the hybrid expression levels relative to the maternal parent and paternal parent, allowing for the identification of maternal or paternal effects on gene expression in the hybrid. The distributions of the d/a values for the six different inbred-hybrid groups were strikingly similar (Figure 6A–B). The d/a type I distribution for all six hybrids is centered at approximately zero, and the distribution tails consistently flattened within the parental range (between -1.0 and 1.0) (Figure 6A). We did note that the center of the d/a type I distribution is skewed slightly towards the low parent. We suspected that the slight deviation of d/a type I values from the mid-parent levels may be caused by technical rather than biological factors. We found that genes with lower expression signals exhibited greater deviation from zero than genes with high expression signals [see Additional file 5]. The d/a type I distribution for genes with at least one genotype signal > 10000 units exhibited no deviation from zero for all six hybrids [see Additional file 5]. These findings suggest that technical factors, such as a slightly non-linear dynamic range among the lower microarray signal intensities, may be causing the slightly skewed distributions.

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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