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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

Chromosomal distribution of nonadditive differentially expressed genes with high-parent dominance (HPD), low-parent dominance (LPD), overdominance (ODO), and underdominance (UDO) on the A genome (a) and C genome (b).
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fig4: Chromosomal distribution of nonadditive differentially expressed genes with high-parent dominance (HPD), low-parent dominance (LPD), overdominance (ODO), and underdominance (UDO) on the A genome (a) and C genome (b).

Mentions: There were 2894 unigenes that mapped to the A genome, 2107 that mapped to the C genome (Figure 4), and 593 that were not assigned to either genome. Chromosomal distribution of DEG numbers in hybrids showed that low-parent domiance (LPD) genes were significantly accumulated on chromosomes A06 and C07 (P < 0.001), while high-parent dominance (HPD) genes were on chromosomes A09 and C08 (P < 0.01). Gene expression variation caused by interspecific hybridization was not randomly distributed along the chromosomes. Therefore, different B. napus-B. rapa chromosome introgression lines can be developed to the further study of heterosis pertaining to specific chromosomes.


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)

Chromosomal distribution of nonadditive differentially expressed genes with high-parent dominance (HPD), low-parent dominance (LPD), overdominance (ODO), and underdominance (UDO) on the A genome (a) and C genome (b).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Chromosomal distribution of nonadditive differentially expressed genes with high-parent dominance (HPD), low-parent dominance (LPD), overdominance (ODO), and underdominance (UDO) on the A genome (a) and C genome (b).
Mentions: There were 2894 unigenes that mapped to the A genome, 2107 that mapped to the C genome (Figure 4), and 593 that were not assigned to either genome. Chromosomal distribution of DEG numbers in hybrids showed that low-parent domiance (LPD) genes were significantly accumulated on chromosomes A06 and C07 (P < 0.001), while high-parent dominance (HPD) genes were on chromosomes A09 and C08 (P < 0.01). Gene expression variation caused by interspecific hybridization was not randomly distributed along the chromosomes. Therefore, different B. napus-B. rapa chromosome introgression lines can be developed to the further study of heterosis pertaining to specific chromosomes.

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