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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

The size distribution of transcriptomic unigenes assembled by the B. rapa (a) and B. oleracea (b).
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fig3: The size distribution of transcriptomic unigenes assembled by the B. rapa (a) and B. oleracea (b).

Mentions: To identify transcripts of P1, P2, and F1, three cDNA libraries were constructed from their leaves and sequenced by Illumina paired-end sequencing. Sequence data from each of the libraries consisted of 6.0 Gb from B. rapa (AA genome), 5.2 Gb from B. napus (AACC genome), and 6.7 Gb from the hybrid (AAC genome). High-quality cleaned raw reads from all of those data were aligned to reference sequences. In total, 67,951,208 reads and 46,207,184 reads were mapped in the B. rapa and B. oleracea reference genomes, respectively. In the B. rapa genome, 38,522 unigenes were assembled with a minimum scaffold size of 200 bp and a total length of 51,995,312 bp, with an average length of 1,349 bp (Figure 3(a)). The B. oleracea genome had a total of 42,009 unigenes with a minimum scaffold size of 300 bp, a total length of 51,691,329 bp, and an average length of 1,230 bp (Figure 3(b)).


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)

The size distribution of transcriptomic unigenes assembled by the B. rapa (a) and B. oleracea (b).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig3: The size distribution of transcriptomic unigenes assembled by the B. rapa (a) and B. oleracea (b).
Mentions: To identify transcripts of P1, P2, and F1, three cDNA libraries were constructed from their leaves and sequenced by Illumina paired-end sequencing. Sequence data from each of the libraries consisted of 6.0 Gb from B. rapa (AA genome), 5.2 Gb from B. napus (AACC genome), and 6.7 Gb from the hybrid (AAC genome). High-quality cleaned raw reads from all of those data were aligned to reference sequences. In total, 67,951,208 reads and 46,207,184 reads were mapped in the B. rapa and B. oleracea reference genomes, respectively. In the B. rapa genome, 38,522 unigenes were assembled with a minimum scaffold size of 200 bp and a total length of 51,995,312 bp, with an average length of 1,349 bp (Figure 3(a)). The B. oleracea genome had a total of 42,009 unigenes with a minimum scaffold size of 300 bp, a total length of 51,691,329 bp, and an average length of 1,230 bp (Figure 3(b)).

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