Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process

Abstract

BackgroundHickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory.ResultsIn our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis.ConclusionsOur comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3182-4) contains supplementary material, which is available to authorized users.

Transcriptomic Analysis Provides Insights into Grafting Union Development in Pecan (Carya illinoinensis)

“…Correspondingly, all the unigenes except one (c147017.graph_c0) encoding auxin influx carrier, and two unigenes (c129281.graph_c0 and c94763.graph_c0) encoding auxin efflux carrier were significantly up-regulated over the course of graft union development ( Figure 5 ). Similarly, genes responsible for auxin transport were induced during the grafting process of grapevine [ 6 ] and hickory [ 8 ]. The accumulated auxin is indispensable for the regulation of callus proliferation and cambial activity [ 14 , 15 ].…”

“…In recent years, RNA sequencing (RNA-seq) is a rapidly emerging transcriptome technology that can be performed without a reference genome. It has been employed to analyze the expression of mRNA and miRNA in hickory graft process, through which candidate genes involved in the auxin and cytokinin signaling were identified [ 8 ]; otherwise, a total of 12 candidate grafting-responsive miRNA were detected [ 9 ]. A comparative proteomic analysis of the hickory graft unions revealed that key enzymes involved in flavonoid biosynthesis were up-regulated 7 days after grafting [ 10 ].…”

Plasma membrane H+‐ATPase activity and graft success of breadfruit (Artocarpus altilis) onto interspecific rootstocks of marang (A. odoratissimus) and pedalai (A. sericicarpus)

“…Up‐regulation of both PM H + ‐ATPase protein and genes was observed in the graft union of Hickory ( Carya cathayensis ; Qiu et al . ; Xu et al . ).…”

Auxin enhances grafting success in Carya cathayensis (Chinese hickory)

“…Successful grafting requires that both xylem and phloem are connected between root stock and scion. In the previous reports, we investigated the transcriptomic and proteomic changes in scion and root stock during grafting (Zheng et al 2010 ; Qiu et al 2016 ; Xu et al 2017 ). In this study, we have demonstrated that IAA treatment improves the grafting success in Chinese hickory.…”

“…The relative expressions in the samples were calculated by means of 2 −ΔΔCq method with 0 day rootstock value as the reference sample. Actin from Chinese hickory was used as a reference gene for the expression analysis (Zheng et al 2010 ; Huang et al 2013 ; Qiu et al 2016 ). The data generated were analyzed by the SPSS 17.0 software (SPSS17 Inc., http://www.spss.com ).…”