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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

The numbers of DEGs between red/green skin color mutant pairs. Up-regulated (red), down-regulated (blue), and Total DEGs (green) were quantified. The results of four comparisons are shown.
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Figure 1: The numbers of DEGs between red/green skin color mutant pairs. Up-regulated (red), down-regulated (blue), and Total DEGs (green) were quantified. The results of four comparisons are shown.

Mentions: To compare differential expression between red and green coloration in pear fruit, we used RPKM to investigate transcript enrichment, which can eliminate the influence of differences in gene length and sequencing level. Furthermore, we employed IDEG6 to identify mRNAs showing statistically significant differences based on their relative abundance. We compared the samples from different colored fruits at the same developmental stage, so that three pairs of comparisons were implemented (Figure 1). Among these comparisons, we found that the most differentially expressed transcripts were between red 1 vs. green 1, with 1032 up-regulated unigenes and 1226 down- regulated unigenes. Simultaneously, anthocyanin content reached peak values at the early stages of fruit development. Fewer unigenes were observed between red 2 and green 2, in which only 835 unigenes were identified. Of these genes, 528 were up- regulated and 307 were down- regulated. In general, compared with green color fruit, a total of 2230 unigenes were significantly differentially expressed. Among all unigenes, 1680 up-regulated unigenes and 550 down-regulated unigenes were identified in red skinned fruits. The plots of unigenes between red and green revealed unigenes with both fold change and significance (Figure 2).


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)

The numbers of DEGs between red/green skin color mutant pairs. Up-regulated (red), down-regulated (blue), and Total DEGs (green) were quantified. The results of four comparisons are shown.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: The numbers of DEGs between red/green skin color mutant pairs. Up-regulated (red), down-regulated (blue), and Total DEGs (green) were quantified. The results of four comparisons are shown.
Mentions: To compare differential expression between red and green coloration in pear fruit, we used RPKM to investigate transcript enrichment, which can eliminate the influence of differences in gene length and sequencing level. Furthermore, we employed IDEG6 to identify mRNAs showing statistically significant differences based on their relative abundance. We compared the samples from different colored fruits at the same developmental stage, so that three pairs of comparisons were implemented (Figure 1). Among these comparisons, we found that the most differentially expressed transcripts were between red 1 vs. green 1, with 1032 up-regulated unigenes and 1226 down- regulated unigenes. Simultaneously, anthocyanin content reached peak values at the early stages of fruit development. Fewer unigenes were observed between red 2 and green 2, in which only 835 unigenes were identified. Of these genes, 528 were up- regulated and 307 were down- regulated. In general, compared with green color fruit, a total of 2230 unigenes were significantly differentially expressed. Among all unigenes, 1680 up-regulated unigenes and 550 down-regulated unigenes were identified in red skinned fruits. The plots of unigenes between red and green revealed unigenes with both fold change and significance (Figure 2).

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