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Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement.

Zhang J, Li G, Li H, Pu X, Jiang J, Chai L, Zheng B, Cui C, Yang Z, Zhu Y, Jiang L - Int J Genomics (2015)

Bottom Line: A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes.A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples.The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.

View Article: PubMed Central - PubMed

Affiliation: Crop Science Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 6110066, China.

ABSTRACT
The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (A(n)A(n)CC genome), B. rapa (A(r)A(r) genome), and its hybrid F1 (A(n)A(r)C genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.

No MeSH data available.


Related in: MedlinePlus

Total numbers of differentially expressed genes between P1, P2, and F1 by Venn diagram analyses (a) and statistics of up- or downregulated genes (b).
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fig5: Total numbers of differentially expressed genes between P1, P2, and F1 by Venn diagram analyses (a) and statistics of up- or downregulated genes (b).

Mentions: There were 1386 significant differentially expressed genes between P1 and F1 samples, 858 genes had increased expression in the F1, and 528 genes had decreased expression. There were 5077 significant differentially expressed genes between P2 and F1 samples, with 3241 genes having increased expression in the F1 and 1836 genes being decreased in expression (Figure 5). Changes to expression from P2 were approximately three times the number of genes compared to from P1. There were more genes with increased expression in the F1 (4098) than with decreased expression (2464) when compared to expression levels in the respective parents. We performed gene ontology (GO) enrichment analysis to test the functional categories for DEGs among P1, P2, and F1 (Figure 6) by AgriGO online tool [23] and R statistical software [20]. There were 10, 12, and 18 functional categories of these transcripts that belonged to the cell component (CC), molecular function (MF), and biological process (BP), respectively. The GO analysis showed that the composition of functional pathways associated with genes showing differential expression was similar when comparing changes from either P1 or P2 with F1.


Transcriptome Analysis of Interspecific Hybrid between Brassica napus and B. rapa Reveals Heterosis for Oil Rape Improvement.

Zhang J, Li G, Li H, Pu X, Jiang J, Chai L, Zheng B, Cui C, Yang Z, Zhu Y, Jiang L - Int J Genomics (2015)

Total numbers of differentially expressed genes between P1, P2, and F1 by Venn diagram analyses (a) and statistics of up- or downregulated genes (b).
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4581553&req=5

fig5: Total numbers of differentially expressed genes between P1, P2, and F1 by Venn diagram analyses (a) and statistics of up- or downregulated genes (b).
Mentions: There were 1386 significant differentially expressed genes between P1 and F1 samples, 858 genes had increased expression in the F1, and 528 genes had decreased expression. There were 5077 significant differentially expressed genes between P2 and F1 samples, with 3241 genes having increased expression in the F1 and 1836 genes being decreased in expression (Figure 5). Changes to expression from P2 were approximately three times the number of genes compared to from P1. There were more genes with increased expression in the F1 (4098) than with decreased expression (2464) when compared to expression levels in the respective parents. We performed gene ontology (GO) enrichment analysis to test the functional categories for DEGs among P1, P2, and F1 (Figure 6) by AgriGO online tool [23] and R statistical software [20]. There were 10, 12, and 18 functional categories of these transcripts that belonged to the cell component (CC), molecular function (MF), and biological process (BP), respectively. The GO analysis showed that the composition of functional pathways associated with genes showing differential expression was similar when comparing changes from either P1 or P2 with F1.

Bottom Line: A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes.A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples.The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.

View Article: PubMed Central - PubMed

Affiliation: Crop Science Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 6110066, China.

ABSTRACT
The hybrid between Brassica napus and B. rapa displays obvious heterosis in both growth performance and stress tolerances. A comparative transcriptome analysis for B. napus (A(n)A(n)CC genome), B. rapa (A(r)A(r) genome), and its hybrid F1 (A(n)A(r)C genome) was carried out to reveal the possible molecular mechanisms of heterosis at the gene expression level. A total of 40,320 nonredundant unigenes were identified using B. rapa (AA genome) and B. oleracea (CC genome) as reference genomes. A total of 6,816 differentially expressed genes (DEGs) were mapped in the A and C genomes with 4,946 DEGs displayed nonadditively by comparing the gene expression patterns among the three samples. The coexistence of nonadditive DEGs including high-parent dominance, low-parent dominance, overdominance, and underdominance was observed in the gene action modes of F1 hybrid, which were potentially related to the heterosis. The coexistence of multiple gene actions in the hybrid was observed and provided a list of candidate genes and pathways for heterosis. The expression bias of transposable element-associated genes was also observed in the hybrid compared to their parents. The present study could be helpful for the better understanding of the determination and regulation of mechanisms of heterosis to aid Brassica improvement.

No MeSH data available.


Related in: MedlinePlus