Characterization of Transcriptional Differences Between Columnar and Standard Apple Trees Using RNA-Seq

Abstract

The columnar apple tree is a valuable resource for genetic improvement of cultivated apples due to its special architecture. To identify genes involved in the columnar architecture, expression profiles of newly developing shoots of standard and columnar trees from a segregating population of “Fuji” × “Telamon” have been analyzed using the new generation of high-throughput RNA-Seq technology. Following Blast analysis against Nr, SwissProt, KEGG, and COG databases, a total of 69,558 unigene annotations have been identified. Among them, more than 80.68% and 79.87% clean reads of Apple-Co and Apple-St samples, respectively, have been mapped to reference apple genome. Interestingly, 57% of genes were covered with more than 50% clean reads. Moreover, 1,252 and 1,443 unigenes from Apple-Co and Apple-St tissues, respectively, had alternative splicing sites. Among these, 614 and 666 were alternative 3′ splice sites and the most abundant, followed by alternative 5′ splice sites, while exon skipping sites were the least frequent. In addition, 13,142 and 13,334 novel transcript units were identified form Apple-Co and Apple-St samples, respectively. Moreover, analysis of RPKM (reads per kilobase per million reads) values found that expression of 5,237 unigenes differed by more than twofold. Among these, 1,359 were enriched in 232 metabolic pathways based on KEGG database annotation, and 2,233 were enriched in biological regulation, cellular process, etc. pathways based on GO functional annotation, and 287 unigenes were related with apple architecture. Among the 287 unigenes, 31 unigenes mapped to chromosome 10 of apple genome, and 25 unigenes were GRAS transcription factor, which were suggested to play an important role in architecture formation of columnar apple trees. Taking together, this study provided a theoretical basis for further enriching gene resources of important agronomic traits of fruit trees and for understanding the formation mechanism of columnar apple trees.