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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

Genes with expression levels validated by qRT-PCR.
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Related In: Results  -  Collection


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fig7: Genes with expression levels validated by qRT-PCR.

Mentions: To assess the accuracy of RNA-seq data, ten differentially expressed unigenes including stress responsive genes, secondary metabolism biosynthesis genes, and epigenetic modifying genes were selected. Three genes belong to underdominance (UDO) and seven genes are belonging to overdominance (ODO) types, which are represented for heterosis analysis. Primer pairs of 10 unigenes for qRT-PCR were designed and listed in Table 4. We tested the similarity between differential gene expression identified by transcriptome and those identified by qRT-PCR. As shown in Figure 7, the qRT-PCR revealed that 8 of 10 genes (except Bol022348 and Bol026880) that showed the differential gene expression level agreed well with the expression patterns of DGE data. Hence, the qRT-PCR results showed general agreement with their transcript abundance changes determined by RNA-seq, which suggested the reliability of the transcriptomic profiling data among the three samples.


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)

Genes with expression levels validated by qRT-PCR.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig7: Genes with expression levels validated by qRT-PCR.
Mentions: To assess the accuracy of RNA-seq data, ten differentially expressed unigenes including stress responsive genes, secondary metabolism biosynthesis genes, and epigenetic modifying genes were selected. Three genes belong to underdominance (UDO) and seven genes are belonging to overdominance (ODO) types, which are represented for heterosis analysis. Primer pairs of 10 unigenes for qRT-PCR were designed and listed in Table 4. We tested the similarity between differential gene expression identified by transcriptome and those identified by qRT-PCR. As shown in Figure 7, the qRT-PCR revealed that 8 of 10 genes (except Bol022348 and Bol026880) that showed the differential gene expression level agreed well with the expression patterns of DGE data. Hence, the qRT-PCR results showed general agreement with their transcript abundance changes determined by RNA-seq, which suggested the reliability of the transcriptomic profiling data among the three samples.

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