Scientia Horticulturae 194 (2015) 7–17 Contents lists available at ScienceDirect Scientia Horticulturae journal homepage: www.elsevier.com/locate/scihorti Differential gene expression analysis of early-ripening mutants of grape (Vitis vinifera L.) Yueyan Wu a,∗ , Tao Fu a,b , Zhonghua Wang a , Caifeng Jiao a , Zhengfeng Yang a , Basharat Ali c , Weijun Zhou c a College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, China b Ningbo City College of Vocational Technology, Ningbo 315502, China c Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou 310058, China a r t i c l e i n f o Article history: Received 23 December 2014 Received in revised form 4 July 2015 Accepted 14 July 2015 Keywords: Grape Digital gene expression Fruit skin color Early ripening a b s t r a c t In the present study, digital gene expression (DGE) profiles of grape (Vitis vinifera L., cv. Yinhong) and its mutants (YH-20-1 and YH-20-2) were constructed to identify the functional genes associated to early- ripening, aroma and peel color. The DGE libraries were established from the leaves of Yinhong and its mutants, and then sequenced by the Illumina/Hisseq technique. The functional analyses of both GO enrichment and KEGG pathway enrichment were performed with transcriptome data as reference. The DGE analysis showed that the 2991 and 5049 different genes were expressed in the mutants (YH-20-1 and YH-20-2) as compared to their parent Yinhong, respectively. Combined with GO annotations and KEGG pathway enrichment analysis, the expression of two early-ripening related genes and six aroma formation related genes was significantly up-regulated in YH-20-1; while, in YH-20-2, only one early-ripening related gene was significantly up-regulated. Moreover, results showed that resistance and neutral amino acid related genes were also up-regulated in both mutants. Further, this study demonstrated that mutant YH-20-1 showed 3-lobed deeper leaf blade, and purple black fruit skin; while, mutant YH-20-2 showed pink fruit skin and denser leaf pubescence. The time-intensity method showed strong fragrance in YH-20- 1 as compared to YH-20-2 and Yinhong. The expression levels of randomly selected genes were confirmed by quantitative real-time PCR. Findings of the present study revealed that both mutants were promising with stronger resistance, early-ripening by showing purple black fruit skin and pink fruit skin than their parent Yinhong, respectively. © 2015 Elsevier B.V. All rights reserved. 1. Introduction Plant resistance and its morphological characteristics (such as leaf pubescence, leaf thickness and plant height) are related to biochemical processes (such as antioxidant enzyme activities and endogenous phytohormone balance) during the growth and devel- opment (Brandstatter and Kieber, 1998; Ori et al., 1999). Genes related to grape (Vitis vinifera L.) morphology, maturity, quality and resistance are very complicated; as the appearance of the plant and phenotype of leaf are closely related to phytohormones. The over-expression of IPT (isopentenyl transferase gene) and KNOX- I (knotted1-like homeobox I gene) in different plants increases the synthesis of cytokinin (Brugiere et al., 2008; Tanaka et al., 2008). The IPT and KNOX-I are regulatory genes which regulate the ∗ Corresponding author. E-mail address: wyy2000@zwu.edu.cn (Y. Wu) synthesis of cytokinins. The over-expression of IPT and/or KNOX-I can also influence the plant appearance and leaf phenotype, includ- ing stunted growth, narrow leaf, splitted edge and loss of symmetry (Brugiere et al., 2008; Tanaka et al., 2008). In addition, over-expression of KNOX-I also reduces the gib- berellins content, which changes the leaf morphology and plant becomes dwarf (Kusaba et al., 1998; Tanakau-Ueguchi et al., 1998). Such kind of phenotype can be reversed by exogenously applied gibberellins (Hay et al., 2002). Moreover, plant adaptation to stress is affected by phytohormones, and a number of genetic factors may change the membrane system and increase the resistance ability against the stress by regulating different genes and metabolisms. The resistance related genes are express significantly under stress conditions, and over-expression of a gene improves the resis- tance of plants against a pathogen, while the over-expression of a transcription factor can activate a number of downstream disease- resistant gene expressions (Marchive et al., 2007; Buxdorf et al., 2014). However, grapes are vulnerable to pathogen infection or http://dx.doi.org/10.1016/j.scienta.2015.07.022 0304-4238/© 2015 Elsevier B.V. All rights reserved.