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Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays.

Gaeta RT, Yoo SY, Pires JC, Doerge RW, Chen ZJ, Osborn TC - PLoS ONE (2009)

Bottom Line: Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization.Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression.In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America.

ABSTRACT

Background: Studies in resynthesized Brassica napus allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S(5ratio6)) alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks.

Methodology/principal findings: We utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S(0ratio1) and S(5ratio6) generations as well as their diploid progenitors B. rapa and B. oleracea. Differential gene expression between the progenitors and additive (midparent) expression in the allopolyploids were tested. The S(5ratio6) lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6-15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6-32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S(0ratio1) lines and 0.1-0.2% were nonadditive among all S(5ratio6) lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S(5ratio6) lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S(0ratio1) lines.

Conclusions/significance: Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization. Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression. In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted.

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Venn Diagrams Summarizing the Number of Differentially Expressed Genes Detected in Each Allopolyploid at the S0∶1 and S5∶6 Generations.The number of differentially expressed genes detected in the S0∶1 and S5∶6 generations (left and right panels, respectively) under the A) per-gene variance ANOVA model, B) common variance ANOVA model, and C) intersection of the per-gene and common variance models.
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pone-0004760-g002: Venn Diagrams Summarizing the Number of Differentially Expressed Genes Detected in Each Allopolyploid at the S0∶1 and S5∶6 Generations.The number of differentially expressed genes detected in the S0∶1 and S5∶6 generations (left and right panels, respectively) under the A) per-gene variance ANOVA model, B) common variance ANOVA model, and C) intersection of the per-gene and common variance models.

Mentions: Under the per-gene ANOVA model, 1.6 to 32% (ave. 11.7%) of all genes displayed nonadditive expression among S0∶1 allopolyploids, and 3.1 to 4.4% (ave. 3.7%) demonstrated nonadditive expression among S5∶6 allopolyploids (Table 1; Datasets S2, S3, S4, S5, S6, S7, S8). Significantly more genes showed up regulation relative to the midparent expression value in comparisons with lines 6400, 5250, and 1250, and significantly more genes were down regulated in comparisons with lines 5200 and 1200 (one sample X2 tests of equal proportions with Bonferroni correction; P<0.00625; Table 1). Only 79 genes (0.3%) and 52 genes (0.2%) reproducibly demonstrated nonadditive expression in all three lines at the S0∶1 and S5∶6 generations, respectively. No significant bias in the number of up or down regulated genes was observed among the 79 and 52 genes that reproducibly changed in three lines at the S0∶1 and S5∶6 generations, respectively. The genes differentially expressed in the allopolyploid comparisons were significantly overrepresented by those differentially expressed between the diploid progenitors (Table 1, see footnote c), and were equally represented by genes up or down regulated in the progenitors (data not shown). The numbers of differentially expressed genes shared among the three lines at the S0∶1 and S5∶6 generations are displayed in Figure 2A. Sixteen genes were differentially expressed in all three lines in both generations under the per-gene ANOVA model, nine of which have no known function (Table S1).


Analysis of gene expression in resynthesized Brassica napus Allopolyploids using arabidopsis 70mer oligo microarrays.

Gaeta RT, Yoo SY, Pires JC, Doerge RW, Chen ZJ, Osborn TC - PLoS ONE (2009)

Venn Diagrams Summarizing the Number of Differentially Expressed Genes Detected in Each Allopolyploid at the S0∶1 and S5∶6 Generations.The number of differentially expressed genes detected in the S0∶1 and S5∶6 generations (left and right panels, respectively) under the A) per-gene variance ANOVA model, B) common variance ANOVA model, and C) intersection of the per-gene and common variance models.
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2651575&req=5

pone-0004760-g002: Venn Diagrams Summarizing the Number of Differentially Expressed Genes Detected in Each Allopolyploid at the S0∶1 and S5∶6 Generations.The number of differentially expressed genes detected in the S0∶1 and S5∶6 generations (left and right panels, respectively) under the A) per-gene variance ANOVA model, B) common variance ANOVA model, and C) intersection of the per-gene and common variance models.
Mentions: Under the per-gene ANOVA model, 1.6 to 32% (ave. 11.7%) of all genes displayed nonadditive expression among S0∶1 allopolyploids, and 3.1 to 4.4% (ave. 3.7%) demonstrated nonadditive expression among S5∶6 allopolyploids (Table 1; Datasets S2, S3, S4, S5, S6, S7, S8). Significantly more genes showed up regulation relative to the midparent expression value in comparisons with lines 6400, 5250, and 1250, and significantly more genes were down regulated in comparisons with lines 5200 and 1200 (one sample X2 tests of equal proportions with Bonferroni correction; P<0.00625; Table 1). Only 79 genes (0.3%) and 52 genes (0.2%) reproducibly demonstrated nonadditive expression in all three lines at the S0∶1 and S5∶6 generations, respectively. No significant bias in the number of up or down regulated genes was observed among the 79 and 52 genes that reproducibly changed in three lines at the S0∶1 and S5∶6 generations, respectively. The genes differentially expressed in the allopolyploid comparisons were significantly overrepresented by those differentially expressed between the diploid progenitors (Table 1, see footnote c), and were equally represented by genes up or down regulated in the progenitors (data not shown). The numbers of differentially expressed genes shared among the three lines at the S0∶1 and S5∶6 generations are displayed in Figure 2A. Sixteen genes were differentially expressed in all three lines in both generations under the per-gene ANOVA model, nine of which have no known function (Table S1).

Bottom Line: Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization.Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression.In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin, United States of America.

ABSTRACT

Background: Studies in resynthesized Brassica napus allopolyploids indicate that homoeologous chromosome exchanges in advanced generations (S(5ratio6)) alter gene expression through the loss and doubling of homoeologous genes within the rearrangements. Rearrangements may also indirectly affect global gene expression if homoeologous copies of gene regulators within rearrangements have differential affects on the transcription of genes in networks.

Methodology/principal findings: We utilized Arabidopsis 70mer oligonucleotide microarrays for exploring gene expression in three resynthesized B. napus lineages at the S(0ratio1) and S(5ratio6) generations as well as their diploid progenitors B. rapa and B. oleracea. Differential gene expression between the progenitors and additive (midparent) expression in the allopolyploids were tested. The S(5ratio6) lines differed in the number of genetic rearrangements, allowing us to test if the number of genes displaying nonadditive expression was related to the number of rearrangements. Estimates using per-gene and common variance ANOVA models indicated that 6-15% of 26,107 genes were differentially expressed between the progenitors. Individual allopolyploids showed nonadditive expression for 1.6-32% of all genes. Less than 0.3% of genes displayed nonadditive expression in all S(0ratio1) lines and 0.1-0.2% were nonadditive among all S(5ratio6) lines. Differentially expressed genes in the polyploids were over-represented by genes differential between the progenitors. The total number of differentially expressed genes was correlated with the number of genetic changes in S(5ratio6) lines under the common variance model; however, there was no relationship using a per-gene variance model, and many genes showed nonadditive expression in S(0ratio1) lines.

Conclusions/significance: Few genes reproducibly demonstrated nonadditive expression among lineages, suggesting few changes resulted from a general response to polyploidization. Furthermore, our microarray analysis did not provide strong evidence that homoeologous rearrangements were a determinant of genome-wide nonadditive gene expression. In light of the inherent limitations of the Arabidopsis microarray to measure gene expression in polyploid Brassicas, further studies are warranted.

Show MeSH