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Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica 'Fuji'.

Wang N, Zheng Y, Duan N, Zhang Z, Ji X, Jiang S, Sun S, Yang L, Bai Y, Fei Z, Chen X - PLoS ONE (2015)

Bottom Line: Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses.Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR.Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China.

ABSTRACT
Transcriptome profiles of the red- and white-fleshed apples in an F1 segregating population of Malus sieversii f.Niedzwetzkyana and M.domestica 'Fuji' were generated using the next-generation high-throughput RNA sequencing (RNA-Seq) technology and compared. A total of 114 differentially expressed genes (DEGs) were obtained, of which 88 were up-regulated and 26 were down-regulated in red-fleshed apples. The 88 up-regulated genes were enriched with those related to flavonoid biosynthetic process and stress responses. Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses. Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR. After exploring the possible regulatory network, we speculated that flavonoid metabolism might be involved in stress responses in red-fleshed apple. Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances.

No MeSH data available.


Related in: MedlinePlus

Verification of DEGs by qRT-PCR.The expression patterns of flavonoid synthesis-related genes in the red- and white-fleshed apples were validated by qRT-PCR. Actin was used as aninternal control.
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pone.0133468.g006: Verification of DEGs by qRT-PCR.The expression patterns of flavonoid synthesis-related genes in the red- and white-fleshed apples were validated by qRT-PCR. Actin was used as aninternal control.

Mentions: To validate the gene expression results obtained from the RNA-Seq analysis, 30 DEGs (20 up-regulated and 10 down-regulated) were selected for qRT-PCR verification (Fig 6). The 20 up-regulated genes included ten related to flavonoid biosynthesis, two encoding MYB (MYB-related)TFs and eight encoding multiple stress responsive proteins. We found that the RPKM values of most of the 20 up-regulated genes were highly consistent with the expression levels obtained by qRT-PCR; the exceptions were MDP0000788934 (encoding ANS), MDP0000252292(encoding GST), MDP0000543445(encoding UFGT) and MDP0000293578(encoding 4CL) (S7 Table). The differential expression levels of these four genes were much higher in the qRT-PCR data. In addition, the expression levels of MDP0000788934, MDP0000252292, MDP0000388415, MDP0000543445, MDP0000175240 and MDP0000293578 was differed by more than 10 times between the red- and white-fleshed apples, indicating that these genes may play a decisive role in the phenotypic development of the red-fleshed apple. Among the 10 down-regulated genes, the RPKM values of MDP0000131249, MDP0000282334 and MDP0000248148 were nearly consistent with the qRT-PCR results, but the expression levels of the other genes were higher in the qRT-PCR results. Despite some quantitative differences in expression levels, the trends of the expression levels were similar in both the RNA-Seq and qRT-PCR data.


Comparative Transcriptomes Analysis of Red- and White-Fleshed Apples in an F1 Population of Malus sieversii f. niedzwetzkyana Crossed with M. domestica 'Fuji'.

Wang N, Zheng Y, Duan N, Zhang Z, Ji X, Jiang S, Sun S, Yang L, Bai Y, Fei Z, Chen X - PLoS ONE (2015)

Verification of DEGs by qRT-PCR.The expression patterns of flavonoid synthesis-related genes in the red- and white-fleshed apples were validated by qRT-PCR. Actin was used as aninternal control.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4514764&req=5

pone.0133468.g006: Verification of DEGs by qRT-PCR.The expression patterns of flavonoid synthesis-related genes in the red- and white-fleshed apples were validated by qRT-PCR. Actin was used as aninternal control.
Mentions: To validate the gene expression results obtained from the RNA-Seq analysis, 30 DEGs (20 up-regulated and 10 down-regulated) were selected for qRT-PCR verification (Fig 6). The 20 up-regulated genes included ten related to flavonoid biosynthesis, two encoding MYB (MYB-related)TFs and eight encoding multiple stress responsive proteins. We found that the RPKM values of most of the 20 up-regulated genes were highly consistent with the expression levels obtained by qRT-PCR; the exceptions were MDP0000788934 (encoding ANS), MDP0000252292(encoding GST), MDP0000543445(encoding UFGT) and MDP0000293578(encoding 4CL) (S7 Table). The differential expression levels of these four genes were much higher in the qRT-PCR data. In addition, the expression levels of MDP0000788934, MDP0000252292, MDP0000388415, MDP0000543445, MDP0000175240 and MDP0000293578 was differed by more than 10 times between the red- and white-fleshed apples, indicating that these genes may play a decisive role in the phenotypic development of the red-fleshed apple. Among the 10 down-regulated genes, the RPKM values of MDP0000131249, MDP0000282334 and MDP0000248148 were nearly consistent with the qRT-PCR results, but the expression levels of the other genes were higher in the qRT-PCR results. Despite some quantitative differences in expression levels, the trends of the expression levels were similar in both the RNA-Seq and qRT-PCR data.

Bottom Line: Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses.Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR.Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances.

View Article: PubMed Central - PubMed

Affiliation: State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China; College of Horticulture Sciences, Shandong Agricultural University, Tai'an, Shandong, China.

ABSTRACT
Transcriptome profiles of the red- and white-fleshed apples in an F1 segregating population of Malus sieversii f.Niedzwetzkyana and M.domestica 'Fuji' were generated using the next-generation high-throughput RNA sequencing (RNA-Seq) technology and compared. A total of 114 differentially expressed genes (DEGs) were obtained, of which 88 were up-regulated and 26 were down-regulated in red-fleshed apples. The 88 up-regulated genes were enriched with those related to flavonoid biosynthetic process and stress responses. Further analysis identified 22 genes associated with flavonoid biosynthetic process and 68 genes that may be related to stress responses. Furthermore, the expression of 20 up-regulated candidate genes (10 related to flavonoid biosynthesis, two encoding MYB transcription factors and eight related to stress responses) and 10 down-regulated genes were validated by quantitative real-time PCR. After exploring the possible regulatory network, we speculated that flavonoid metabolism might be involved in stress responses in red-fleshed apple. Our findings provide a theoretical basis for further enriching gene resources associated with flavonoid synthesis and stress responses of fruit trees and for breeding elite apples with high flavonoid content and/or increased stress tolerances.

No MeSH data available.


Related in: MedlinePlus