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

Zongying Zhang,Jingxuan Liu,Shasha Sun,Shenghui Jiang,Zhangjun Fei,Sumin Qi,Xiaohao Ji,Xuesen Chen,Shujing Wu,Min Li,Shouqian Feng,Nan Wang,Deyun Wang,Haifeng Xu,Xianlong Zhang

doi:10.1371/journal.pone.0146061

Zongying Zhang, Jingxuan Liu + Show 13 more

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https://doi.org/10.1371/journal.pone.0146061

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Journal: PloS one	Publication Date: Dec 31, 2015
Citations: 22	License type: CC BY 4.0

Affiliation: Shandong Agricultural University, Cornell University

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.

Highlights

Apple (Malus domestica) is one of the most economically important and widely cultivated horticultural fruit crops worldwide
Samples at 60 days after full bloom (DAFB) and 70 DAFB were used for construction of suppression hybridization (SSH) libraries to identify differentially expressed genes involved in fruit ripening and softening
We propose that apple cultivars can be divided into three types according to sensitivity to ethylene: ethylene-insensitive (‘Fuji’ e.g.), ethyleneintermediate (‘Golden Delicious’ e.g.) and ethylene-sensitive (‘Taishanzaoxia’, ‘Jonagold’ e.g.) [28]

Summary

Introduction

Apple (Malus domestica) is one of the most economically important and widely cultivated horticultural fruit crops worldwide. The fruits are rich in nutrients, non-nutrient components, polyphenols and other phytochemicals beneficial for human health [1]. Fruit softening represents a major quality problem for apples in the marketplace. Fruit softening is undesirable as it results in decreased shelf life and lower sensory values [2]. The extent of fruit softening varies greatly among cultivars and the maintenance of fruit firmness is an important trait in apple breeding programs. Extensive research on the metabolic processes and molecular mechanisms involved in ethylene production, ethylene signaling pathway, fruit ripening and softening have been carried out, but a full understanding of these processes and the mechanisms responsible in different apple cultivars remains incomplete [3,4,5]

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