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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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Related in: MedlinePlus

Distribution of the number of EST members in each unigene.
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pone.0146061.g002: Distribution of the number of EST members in each unigene.

Mentions: A total of 1032 clones (504 clones in forward library and 528 clones in reverse library) were selected and sequenced, with the positive rate of 89% and 88%, respectively. After removal of low-quality sequences and sequences of bacterial origin, 918 high-quality ESTs ranging between 200 and 1000 bp were obtained, with an average length of 421 bp. These ESTs were further assembled into 648 unigenes, with an average length of 437 bp, among which 67 were contigs (assembled from multiple EST sequences) and 581 were singletons (sequences that could not be assembled into a contig) (Table 1). The number of EST members in unigenes varied from one to 96, with most of the unigenes (581, 90%) present in low copy numbers. Most contigs obtained (70.1%) were composed of two ESTs (Fig 2).


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)

Distribution of the number of EST members in each unigene.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0146061.g002: Distribution of the number of EST members in each unigene.
Mentions: A total of 1032 clones (504 clones in forward library and 528 clones in reverse library) were selected and sequenced, with the positive rate of 89% and 88%, respectively. After removal of low-quality sequences and sequences of bacterial origin, 918 high-quality ESTs ranging between 200 and 1000 bp were obtained, with an average length of 421 bp. These ESTs were further assembled into 648 unigenes, with an average length of 437 bp, among which 67 were contigs (assembled from multiple EST sequences) and 581 were singletons (sequences that could not be assembled into a contig) (Table 1). The number of EST members in unigenes varied from one to 96, with most of the unigenes (581, 90%) present in low copy numbers. Most contigs obtained (70.1%) were composed of two ESTs (Fig 2).

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