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Article|01 Oct 2014|OPEN
Genomic variants of genes associated with three horticultural traits in apple revealed by genome re-sequencing
Weiping Chen1 , Lu Xin2 , Zhihong Gao2 , Yingjun Hou2 , Xinyi Yu2 , Zhen Zhang2 , Shijie Zhang2 and Shenchun Qu,2 ,
1College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
2College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
*Corresponding author. E-mail:

Horticulture Research 1,
Article number: 45 (2014)
Views: 673

Received: 28 Apr 2014
Revised: 06 Jun 2014
Accepted: 25 Jul 2014
Published online: 01 Oct 2014


The apple (Malus × domestica Borkh.) cultivar ‘Su Shuai’ exhibits greater disease resistance, shorter internodes and lighter fruit flavor compared with its parents ‘Golden Delicious’ and ‘Indo’. To obtain a comprehensive overview of the sequence variation in these three horticultural traits, the genomes of ‘Su Shuai’ and ‘Indo’ were resequenced using next-generation sequencing and compared to the genome of ‘Golden Delicious’. A wide range of genetic variations were detected, including 2 454 406 and 18 749 349 single nucleotide polymorphism (SNP) and 59 547 and 50 143 structural variants (SVs) in the ‘Indo’ and ‘Su Shuai’ genomes, respectively. Among the SVs in ‘Su Shuai’, 17 genes related to disease resistance, 10 genes related to Gibberellin (GA) and 19 genes associated with fruit flavor were identified. The expression patterns of eight of the SV genes were examined using reverse transcription-quantitative polymerase chain reaction (RT-qPCR). The results of this study illustrate the genomic variation in these cultivars and provide evidence for a genetic basis for the horticultural traits of disease resistance, short internodes and lighter flavor exhibited in these cultivars. These results provide a genetic basis for the phenotypic characteristics of ‘Su Shuai’ and, as such, these SVs could serve as gene-specific molecular markers in maker-assisted breeding of apples.