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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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Relationship between parental genetic diversity and differential gene expression. The number of differentially expressed genes identified for each inbred-hybrid group based on stringent statistical criteria is plotted against the genetic distance between parents. Spots representing crosses between stiff stalk (SS) and non-stiff stalk (NSS) groups are shown in red, and spots representing crosses within either group are shown in blue. The Pearson's R correlation value and p-value of the regression are shown.
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Figure 4: Relationship between parental genetic diversity and differential gene expression. The number of differentially expressed genes identified for each inbred-hybrid group based on stringent statistical criteria is plotted against the genetic distance between parents. Spots representing crosses between stiff stalk (SS) and non-stiff stalk (NSS) groups are shown in red, and spots representing crosses within either group are shown in blue. The Pearson's R correlation value and p-value of the regression are shown.

Mentions: Genes that were differentially expressed (DE) among genotypes were identified within each inbred-hybrid group, based on an ANOVA FDR < 0.05 (and minimum signal and fold-change filters; see Methods). The numbers of DE genes were variable among the inbred-hybrid groups (Table 1). There was a strong correlation between the number of DE genes and the level of genetic distance between the parents (Figure 4). The comparison between inbred B84, inbred B73 and hybrid B84 × B73 identified 290 DE genes, by far the lowest number of any group. The comparison between inbred B37, inbred B73 and hybrid B37 × B73 identified 655 DE genes, and the remaining comparisons generated between 885–1071 DE genes (Table 1; Figure 4).


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)

Relationship between parental genetic diversity and differential gene expression. The number of differentially expressed genes identified for each inbred-hybrid group based on stringent statistical criteria is plotted against the genetic distance between parents. Spots representing crosses between stiff stalk (SS) and non-stiff stalk (NSS) groups are shown in red, and spots representing crosses within either group are shown in blue. The Pearson's R correlation value and p-value of the regression are shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Relationship between parental genetic diversity and differential gene expression. The number of differentially expressed genes identified for each inbred-hybrid group based on stringent statistical criteria is plotted against the genetic distance between parents. Spots representing crosses between stiff stalk (SS) and non-stiff stalk (NSS) groups are shown in red, and spots representing crosses within either group are shown in blue. The Pearson's R correlation value and p-value of the regression are shown.
Mentions: Genes that were differentially expressed (DE) among genotypes were identified within each inbred-hybrid group, based on an ANOVA FDR < 0.05 (and minimum signal and fold-change filters; see Methods). The numbers of DE genes were variable among the inbred-hybrid groups (Table 1). There was a strong correlation between the number of DE genes and the level of genetic distance between the parents (Figure 4). The comparison between inbred B84, inbred B73 and hybrid B84 × B73 identified 290 DE genes, by far the lowest number of any group. The comparison between inbred B37, inbred B73 and hybrid B37 × B73 identified 655 DE genes, and the remaining comparisons generated between 885–1071 DE genes (Table 1; Figure 4).

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