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Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

Zhang Z, Jiang S, Wang N, Li M, Ji X, Sun S, Liu J, Wang D, Xu H, Qi S, Wu S, Fei Z, Feng S, Chen X - PLoS ONE (2015)

Bottom Line: These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated.Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'.The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

View Article: PubMed Central - PubMed

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

ABSTRACT
Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88%) were assigned to the biological process category, 356 unigenes (80%) were classified in the molecular function category, and 381 unigenes (86%) were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

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(A) Functional classification of differentially expressed unigenes into GO slim categories. (B) Expression analysis of selected unigenes during the fruit development period.CAD: cinnamyl alcohol dehydrogenase, 4CL: 4-coumarate-CoA ligase, ANR: anthocyanidin reductase-like, C4H: cinnamic acid hydroxylase, FAD2: fatty acid desaturase 2, FAD5: fatty acid desaturase 5, LOX: lipoxygenase, AM: β-amylase.
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pone.0146061.g004: (A) Functional classification of differentially expressed unigenes into GO slim categories. (B) Expression analysis of selected unigenes during the fruit development period.CAD: cinnamyl alcohol dehydrogenase, 4CL: 4-coumarate-CoA ligase, ANR: anthocyanidin reductase-like, C4H: cinnamic acid hydroxylase, FAD2: fatty acid desaturase 2, FAD5: fatty acid desaturase 5, LOX: lipoxygenase, AM: β-amylase.

Mentions: In the biological process category, ‘cellular process’ was the most prevalent (9% of sequences), followed by ‘biosynthesis process’ (7%) and ‘response to stress’ (6%). In addition, ‘fruit ripening’ (0.1%), regulation of gene expression (0.5%), secondary metabolic process (1.7%) and signal transduction (2.4%) were also identified in the biological process category. In the molecular function category, ‘binding’ was the most prevalent (16%) and ‘hydrolase activity’ (10%), ‘sequence-specific DNA binding transcription factor activity’ (1.1%) and ‘transporter activity’ (2.5%) were also identified. In the cellular component category, ‘membrane’ (12%) was the most dominant term, followed by ‘cell wall’ (3%) (Fig 4A).


Identification of Differentially Expressed Genes Associated with Apple Fruit Ripening and Softening by Suppression Subtractive Hybridization.

Zhang Z, Jiang S, Wang N, Li M, Ji X, Sun S, Liu J, Wang D, Xu H, Qi S, Wu S, Fei Z, Feng S, Chen X - PLoS ONE (2015)

(A) Functional classification of differentially expressed unigenes into GO slim categories. (B) Expression analysis of selected unigenes during the fruit development period.CAD: cinnamyl alcohol dehydrogenase, 4CL: 4-coumarate-CoA ligase, ANR: anthocyanidin reductase-like, C4H: cinnamic acid hydroxylase, FAD2: fatty acid desaturase 2, FAD5: fatty acid desaturase 5, LOX: lipoxygenase, AM: β-amylase.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4697835&req=5

pone.0146061.g004: (A) Functional classification of differentially expressed unigenes into GO slim categories. (B) Expression analysis of selected unigenes during the fruit development period.CAD: cinnamyl alcohol dehydrogenase, 4CL: 4-coumarate-CoA ligase, ANR: anthocyanidin reductase-like, C4H: cinnamic acid hydroxylase, FAD2: fatty acid desaturase 2, FAD5: fatty acid desaturase 5, LOX: lipoxygenase, AM: β-amylase.
Mentions: In the biological process category, ‘cellular process’ was the most prevalent (9% of sequences), followed by ‘biosynthesis process’ (7%) and ‘response to stress’ (6%). In addition, ‘fruit ripening’ (0.1%), regulation of gene expression (0.5%), secondary metabolic process (1.7%) and signal transduction (2.4%) were also identified in the biological process category. In the molecular function category, ‘binding’ was the most prevalent (16%) and ‘hydrolase activity’ (10%), ‘sequence-specific DNA binding transcription factor activity’ (1.1%) and ‘transporter activity’ (2.5%) were also identified. In the cellular component category, ‘membrane’ (12%) was the most dominant term, followed by ‘cell wall’ (3%) (Fig 4A).

Bottom Line: These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated.Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'.The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

View Article: PubMed Central - PubMed

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

ABSTRACT
Apple is one of the most economically important horticultural fruit crops worldwide. It is critical to gain insights into fruit ripening and softening to improve apple fruit quality and extend shelf life. In this study, forward and reverse suppression subtractive hybridization libraries were generated from 'Taishanzaoxia' apple fruits sampled around the ethylene climacteric to isolate ripening- and softening-related genes. A set of 648 unigenes were derived from sequence alignment and cluster assembly of 918 expressed sequence tags. According to gene ontology functional classification, 390 out of 443 unigenes (88%) were assigned to the biological process category, 356 unigenes (80%) were classified in the molecular function category, and 381 unigenes (86%) were allocated to the cellular component category. A total of 26 unigenes differentially expressed during fruit development period were analyzed by quantitative RT-PCR. These genes were involved in cell wall modification, anthocyanin biosynthesis, aroma production, stress response, metabolism, transcription, or were non-annotated. Some genes associated with cell wall modification, anthocyanin biosynthesis and aroma production were up-regulated and significantly correlated with ethylene production, suggesting that fruit texture, coloration and aroma may be regulated by ethylene in 'Taishanzaoxia'. Some of the identified unigenes associated with fruit ripening and softening have not been characterized in public databases. The results contribute to an improved characterization of changes in gene expression during apple fruit ripening and softening.

Show MeSH
Related in: MedlinePlus