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Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.).

Yang Y, Yao G, Yue W, Zhang S, Wu J - Front Plant Sci (2015)

Bottom Line: Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin.In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant.This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. "Starkrimson" (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

No MeSH data available.


Related in: MedlinePlus

Functional categorization of genes with significant transcriptional changes between red and green fruit. Purple indicates up-regulated and red indicated down-regulated genes.
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Figure 3: Functional categorization of genes with significant transcriptional changes between red and green fruit. Purple indicates up-regulated and red indicated down-regulated genes.

Mentions: Gene Ontology (GO) is an international standardized gene function classification system that describes properties of genes and their products in any organism. In order to create a profile of gene expression in red-skinned pear, we used WEGO (Web Gene Ontology Annotation Plot) for gene annotation analysis. To screen the candidate genes of DEGs from the transcripts of functional annotation, we analyzed the 4886 differential transcripts at three developmental stages from a total of 174,810 transcripts in the red/green color mutant pair. The DEGs were categorized into 28 functional groups on the basis of their biological processes (Figure 3). The major subcategories were as follows: Seven subcategories for cellular location; eight subcategories for molecular function, and 13 subcategories for biological process. The DEGs in “binding,” “catalytic activity,” “metabolic process,” and “cellular process,” “cell,” “cell part,” and “pigmentation” played important roles during the pigment metabolic process. The results provided a comprehensive view for screening candidate genes related to anthocyanin biosynthesis and metabolic process of red/green color pear fruit. Taking into account that anthocyanin content of red color fruit at different developmental stages is higher than in the green mutant, we searched for DEGs at the three developmental stages, and found that among all of differentially expressed genes, there are seven up-regulated and three down-regulated genes with significant differences at all three stages (Table 3). In the up-regulated unigenes, Pbr013927.1 is an AP2/ERF domain sequence-specific DNA binding transcription factor and Pbr039146.1 and Pbr008092.1 are transporters from proton-dependent oligopeptide transporter and sugar/inositol transporter families. In addition, there were three unigenes encoding enzymes, oxoglutarate/iron-dependent dioxygenase (Pbr021636.1), alcohol dehydrogenase (Pbr021220.1), glutathione S-transferase (GST) (Pbr012649.1), and a hypothetical protein (Pbr039734.1) with unknown function also up-regulated. The three down-regulated unigenes were protein kinase activity (Pbr041919.1), RNA recognition motif domain protein (Pbr041849.1) and mitochondrial carrier protein (Pbr019417.1).


Transcriptome profiling reveals differential gene expression in proanthocyanidin biosynthesis associated with red/green skin color mutant of pear (Pyrus communis L.).

Yang Y, Yao G, Yue W, Zhang S, Wu J - Front Plant Sci (2015)

Functional categorization of genes with significant transcriptional changes between red and green fruit. Purple indicates up-regulated and red indicated down-regulated genes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4588701&req=5

Figure 3: Functional categorization of genes with significant transcriptional changes between red and green fruit. Purple indicates up-regulated and red indicated down-regulated genes.
Mentions: Gene Ontology (GO) is an international standardized gene function classification system that describes properties of genes and their products in any organism. In order to create a profile of gene expression in red-skinned pear, we used WEGO (Web Gene Ontology Annotation Plot) for gene annotation analysis. To screen the candidate genes of DEGs from the transcripts of functional annotation, we analyzed the 4886 differential transcripts at three developmental stages from a total of 174,810 transcripts in the red/green color mutant pair. The DEGs were categorized into 28 functional groups on the basis of their biological processes (Figure 3). The major subcategories were as follows: Seven subcategories for cellular location; eight subcategories for molecular function, and 13 subcategories for biological process. The DEGs in “binding,” “catalytic activity,” “metabolic process,” and “cellular process,” “cell,” “cell part,” and “pigmentation” played important roles during the pigment metabolic process. The results provided a comprehensive view for screening candidate genes related to anthocyanin biosynthesis and metabolic process of red/green color pear fruit. Taking into account that anthocyanin content of red color fruit at different developmental stages is higher than in the green mutant, we searched for DEGs at the three developmental stages, and found that among all of differentially expressed genes, there are seven up-regulated and three down-regulated genes with significant differences at all three stages (Table 3). In the up-regulated unigenes, Pbr013927.1 is an AP2/ERF domain sequence-specific DNA binding transcription factor and Pbr039146.1 and Pbr008092.1 are transporters from proton-dependent oligopeptide transporter and sugar/inositol transporter families. In addition, there were three unigenes encoding enzymes, oxoglutarate/iron-dependent dioxygenase (Pbr021636.1), alcohol dehydrogenase (Pbr021220.1), glutathione S-transferase (GST) (Pbr012649.1), and a hypothetical protein (Pbr039734.1) with unknown function also up-regulated. The three down-regulated unigenes were protein kinase activity (Pbr041919.1), RNA recognition motif domain protein (Pbr041849.1) and mitochondrial carrier protein (Pbr019417.1).

Bottom Line: Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin.In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant.This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University Nanjing, China.

ABSTRACT
Anthocyanin concentration is the key determinant for red skin color in pear fruit. However, the molecular basis for development of red skin is complicated and has not been well-understood thus far. "Starkrimson" (Pyrus communis L.), an introduced red pear cultivated in the north of China and its green mutant provides a desirable red/green pair for identification of candidate genes involved in color variation. Here, we sequenced and annotated the transcriptome for the red/green color mutant at three stages of development using Illumina RNA-seq technology. The total number of mapped reads ranged from 26 to 46 million in six libraries. About 70.11-71.95% of clean reads could be mapped to the reference genome. Compared with green colored fruit, a total of 2230 differentially expressed genes (DEGs) were identified in red fruit. Gene Ontology (GO) terms were defined for 4886 differential transcripts involved in 15 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Three DEGs were identified as candidate genes in the flavonoid pathway, LAR, ANR, and C3H. Tellingly, higher expression was found for genes encoding ANR and LAR in the green color mutant, promoting the proanthocyanidin (PA) pathway and leading to lower anthocyanin. MYB-binding cis-motifs were identified in the promoter region of LAR and ANR. Based on these findings, we speculate that the regulation of PA biosynthesis might be a key factor for this red/green color mutant. Besides the known MYB and MADS transcription families, two new families, AP2 and WRKY, were identified as having high correlation with anthocyanin biosynthesis in red skinned pear. In addition, qRT-PCR was used to confirm the transcriptome results for 17 DEGs, high correlation of gene expression, further proved that AP2 and WARK regulated the anthocyanin biosynthesis in red skinned "Starkrimson," and ANR and LAR promote PA biosynthesis and contribute to the green skinned variant. This study can serve as a valuable new resource laying a solid foundation for functional gene identification in the anthocyanin pathway of red-skinned pear and provide a good reference for relevant research on molecular mechanisms of color variation in other pear species.

No MeSH data available.


Related in: MedlinePlus