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Genome-wide transcriptome profiles of rice hybrids and their parents.

E Z, Huang S, Zhang Y, Ge L, Wang L - Int J Mol Sci (2014)

Bottom Line: Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes.These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages.Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families.

View Article: PubMed Central - PubMed

Affiliation: China National Rice Research Institute, Hangzhou 310006, China. ezhiguo@caas.cn.

ABSTRACT
Heterosis is a widely studied phenomenon in several plant species. However, its genetic basis still remains to be elucidated. In this study, we used RNA-seq data from two rice genotypes and their reciprocal hybrids, and used a combination of transcriptome profiling and allele-specific expression analysis to identify genes that are differentially expressed in the hybrids and their parents or expressed in an allele-specific manner. The differentially expressed genes (DEGs) were identified by a pairwise comparison of the four genotypes. Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes. A total of 1033 (10.24%) of 10,195 genes with informative single nucleotide polymorphism (SNPs) were identified as ASE genes. These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages. Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families. These ASE transcription factors may act in trans to regulate gene expression in filial 1 (F1) hybrids. Our analyses provide a comprehensive transcriptome profile of rice hybrids and their parents, and would be a useful resource for the rice research community.

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The number of genes that were detected by at least one read is indicated for each genotype in the Venn diagram. Four genotypes are shown in different colors. # means the number.
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ijms-15-20833-f001: The number of genes that were detected by at least one read is indicated for each genotype in the Venn diagram. Four genotypes are shown in different colors. # means the number.

Mentions: RNA-seq data provides transcriptome profiles of rice hybrids and their parents. RNA-seq data for seedlings of NPB, 93-11 and their reciprocal hybrids have been generated in previous studies [4]. A total of 311 million reads were generated for 4 fully expanded leaves from 6-week-old plants of the four genotypes. We downloaded reads of four genotypes from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI). Reads from RNA-seq data were aligned to the NPB reference genome (Build 6.1). About 248 (79.74%) million reads were uniquely aligned to Nipponbare reference genome, ranging from 55 to 68 million reads for the four genotypes (Table 1). We also found that 24,017 of 35,119 (68.38%) annotated genes in the NPB reference genome were detected by at least one uniquely mapped read in at least one of the four genotypes, with 33,505 annotated genes in NPB, 32,531 in 93-11, 34,895 in NPB × 93-11 and 93-11 × NPB (Figure 1). In both hybrids, NPB × 93-11 and 93-11 × NPB, more genes were detected with RNA-seq reads than their parents. A similar result (Figure S1) was obtained when we used RNA-seq data of seedling shoots at the four-leaf stage from 4-week-old plants of the four genotypes [5]. These results indicate that more genes were expressed in hybrid progenies than in their parents.


Genome-wide transcriptome profiles of rice hybrids and their parents.

E Z, Huang S, Zhang Y, Ge L, Wang L - Int J Mol Sci (2014)

The number of genes that were detected by at least one read is indicated for each genotype in the Venn diagram. Four genotypes are shown in different colors. # means the number.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4264198&req=5

ijms-15-20833-f001: The number of genes that were detected by at least one read is indicated for each genotype in the Venn diagram. Four genotypes are shown in different colors. # means the number.
Mentions: RNA-seq data provides transcriptome profiles of rice hybrids and their parents. RNA-seq data for seedlings of NPB, 93-11 and their reciprocal hybrids have been generated in previous studies [4]. A total of 311 million reads were generated for 4 fully expanded leaves from 6-week-old plants of the four genotypes. We downloaded reads of four genotypes from Sequence Read Archive (SRA) in National Center for Biotechnology Information (NCBI). Reads from RNA-seq data were aligned to the NPB reference genome (Build 6.1). About 248 (79.74%) million reads were uniquely aligned to Nipponbare reference genome, ranging from 55 to 68 million reads for the four genotypes (Table 1). We also found that 24,017 of 35,119 (68.38%) annotated genes in the NPB reference genome were detected by at least one uniquely mapped read in at least one of the four genotypes, with 33,505 annotated genes in NPB, 32,531 in 93-11, 34,895 in NPB × 93-11 and 93-11 × NPB (Figure 1). In both hybrids, NPB × 93-11 and 93-11 × NPB, more genes were detected with RNA-seq reads than their parents. A similar result (Figure S1) was obtained when we used RNA-seq data of seedling shoots at the four-leaf stage from 4-week-old plants of the four genotypes [5]. These results indicate that more genes were expressed in hybrid progenies than in their parents.

Bottom Line: Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes.These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages.Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families.

View Article: PubMed Central - PubMed

Affiliation: China National Rice Research Institute, Hangzhou 310006, China. ezhiguo@caas.cn.

ABSTRACT
Heterosis is a widely studied phenomenon in several plant species. However, its genetic basis still remains to be elucidated. In this study, we used RNA-seq data from two rice genotypes and their reciprocal hybrids, and used a combination of transcriptome profiling and allele-specific expression analysis to identify genes that are differentially expressed in the hybrids and their parents or expressed in an allele-specific manner. The differentially expressed genes (DEGs) were identified by a pairwise comparison of the four genotypes. Detailed annotation of DEGs suggested that these genes showed enrichment in some gene ontology categories, and they tend to have tissue-specific expression patterns compared to all genes. A total of 1033 (10.24%) of 10,195 genes with informative single nucleotide polymorphism (SNPs) were identified as ASE genes. These allele-specific expessed (ASE) genes showed a broader expression breadth suggesting that they function in diverse developmental stages. Among 1033 ASE genes, we also identified 45 ASE transcription factors belonging to 17 transcription factor families. These ASE transcription factors may act in trans to regulate gene expression in filial 1 (F1) hybrids. Our analyses provide a comprehensive transcriptome profile of rice hybrids and their parents, and would be a useful resource for the rice research community.

Show MeSH