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Profiling expression changes caused by a segmental aneuploid in maize.

Makarevitch I, Phillips RL, Springer NM - BMC Genomics (2008)

Bottom Line: Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves.Expression profiling revealed that approximately 40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage.We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St, Paul MN 55108, USA. springer@umn.edu.

ABSTRACT

Background: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated.

Results: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that approximately 40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage.

Conclusion: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.

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Developmental expression pattern of the knox10 gene in wild-type B73 tissues. RT-PCR was performed to detect expression of the knox10 gene in cDNA derived from 11-day post pollination endosperm, 3-day post pollination whole kernels, 11-day post pollination whole kernels, 14 day seedlings, roots, immature ear, mature leaf and immature tassel. Expression is detection in every plant tissue containing apical meristems except for roots. The lower image is a loading control showing similar levels of transcript detected in these samples using primers for the aat gene.
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Figure 6: Developmental expression pattern of the knox10 gene in wild-type B73 tissues. RT-PCR was performed to detect expression of the knox10 gene in cDNA derived from 11-day post pollination endosperm, 3-day post pollination whole kernels, 11-day post pollination whole kernels, 14 day seedlings, roots, immature ear, mature leaf and immature tassel. Expression is detection in every plant tissue containing apical meristems except for roots. The lower image is a loading control showing similar levels of transcript detected in these samples using primers for the aat gene.

Mentions: Knotting can be caused by ectopic expression of class 1 knotted-like (knox) genes that act as meristem-identity genes in developing leaf tissue [25-27]. A subset of the knox genes, the class I knox genes, show expression specifically in the meristem tissue [22]. However, prolonged ectopic expression of knox genes in differentiating leaf primordia is thought to lead to aberrant differentiation of some cells in the leaf blade resulting in the acquisition of sheath or ligule identity [27]. The maize genome contains at least 13 knox genes (class 1: kn1, rs1, lg3, knox3, knox4, knox5, knox8, knox10, and knox11; and class 2: knox1, knox2, knox6, and knox7) [22], with one gene, knox10, located in the trisomic region of DpDf plants (180 cM – IBM2 2004 neighbors genetic map). The knox6 gene is also located on chromosome 5 but proximal to the translocation breakpoint (IBM2 2004 neighbors genetic map). We investigated the expression of all nine class 1 knotted-like maize genes in the meristematic and leaf tissue of the normal and DpDf 11-day old maize seedlings by RT-PCR (Figure 6). All nine of the investigated knox genes exhibited detectable expression in meristematic tissue of both normal and DpDf plants. We were not able to detect expression for any of these nine genes in developing and mature leaf tissue of wild-type plants. In DpDf plants, ectopic expression of knox10 was detected in developing and mature leaf tissues while expression of the other eight genes was not detected in these tissues (Figure 6). The microarray profiling of the expression levels (see above) for the four class 2 knox genes, knox1, knox2, knox6, and knox7 showed no changes in DpDf plants compared to their normal siblings in whole seedling tissues. Therefore, only the knox10 gene was expressed in leaves of DpDf plants suggesting that the change in expression pattern of knox10 is responsible for the leaf knotting phenotype.


Profiling expression changes caused by a segmental aneuploid in maize.

Makarevitch I, Phillips RL, Springer NM - BMC Genomics (2008)

Developmental expression pattern of the knox10 gene in wild-type B73 tissues. RT-PCR was performed to detect expression of the knox10 gene in cDNA derived from 11-day post pollination endosperm, 3-day post pollination whole kernels, 11-day post pollination whole kernels, 14 day seedlings, roots, immature ear, mature leaf and immature tassel. Expression is detection in every plant tissue containing apical meristems except for roots. The lower image is a loading control showing similar levels of transcript detected in these samples using primers for the aat gene.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2254597&req=5

Figure 6: Developmental expression pattern of the knox10 gene in wild-type B73 tissues. RT-PCR was performed to detect expression of the knox10 gene in cDNA derived from 11-day post pollination endosperm, 3-day post pollination whole kernels, 11-day post pollination whole kernels, 14 day seedlings, roots, immature ear, mature leaf and immature tassel. Expression is detection in every plant tissue containing apical meristems except for roots. The lower image is a loading control showing similar levels of transcript detected in these samples using primers for the aat gene.
Mentions: Knotting can be caused by ectopic expression of class 1 knotted-like (knox) genes that act as meristem-identity genes in developing leaf tissue [25-27]. A subset of the knox genes, the class I knox genes, show expression specifically in the meristem tissue [22]. However, prolonged ectopic expression of knox genes in differentiating leaf primordia is thought to lead to aberrant differentiation of some cells in the leaf blade resulting in the acquisition of sheath or ligule identity [27]. The maize genome contains at least 13 knox genes (class 1: kn1, rs1, lg3, knox3, knox4, knox5, knox8, knox10, and knox11; and class 2: knox1, knox2, knox6, and knox7) [22], with one gene, knox10, located in the trisomic region of DpDf plants (180 cM – IBM2 2004 neighbors genetic map). The knox6 gene is also located on chromosome 5 but proximal to the translocation breakpoint (IBM2 2004 neighbors genetic map). We investigated the expression of all nine class 1 knotted-like maize genes in the meristematic and leaf tissue of the normal and DpDf 11-day old maize seedlings by RT-PCR (Figure 6). All nine of the investigated knox genes exhibited detectable expression in meristematic tissue of both normal and DpDf plants. We were not able to detect expression for any of these nine genes in developing and mature leaf tissue of wild-type plants. In DpDf plants, ectopic expression of knox10 was detected in developing and mature leaf tissues while expression of the other eight genes was not detected in these tissues (Figure 6). The microarray profiling of the expression levels (see above) for the four class 2 knox genes, knox1, knox2, knox6, and knox7 showed no changes in DpDf plants compared to their normal siblings in whole seedling tissues. Therefore, only the knox10 gene was expressed in leaves of DpDf plants suggesting that the change in expression pattern of knox10 is responsible for the leaf knotting phenotype.

Bottom Line: Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves.Expression profiling revealed that approximately 40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage.We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes.

View Article: PubMed Central - HTML - PubMed

Affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, St, Paul MN 55108, USA. springer@umn.edu.

ABSTRACT

Background: While changes in chromosome number that result in aneuploidy are associated with phenotypic consequences such as Down syndrome and cancer, the molecular causes of specific phenotypes and genome-wide expression changes that occur in aneuploids are still being elucidated.

Results: We employed a segmental aneuploid condition in maize to study phenotypic and gene expression changes associated with aneuploidy. Maize plants that are trisomic for 90% of the short arm of chromosome 5 and monosomic for a small distal portion of the short arm of chromosome 6 exhibited a phenotypic syndrome that includes reduced stature, tassel morphology changes and the presence of knots on the leaves. The knotted-like homeobox gene knox10, which is located on the short arm of chromosome 5, was shown to be ectopically expressed in developing leaves of the aneuploid plants. Expression profiling revealed that approximately 40% of the expressed genes in the trisomic region exhibited the expected 1.5 fold increased transcript levels while the remaining 60% of genes did not show altered expression even with increased gene dosage.

Conclusion: We found that the majority of genes with altered expression levels were located within the chromosomal regions affected by the segmental aneuploidy and exhibits dosage-dependent expression changes. A small number of genes exhibit higher levels of expression change not predicted by the dosage, or display altered expression even though they are not located in the aneuploid regions.

Show MeSH
Related in: MedlinePlus