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To obtain insight into potential mechanisms underlying the influence of rootstock on scion growth, we performed a comparative analysis of ‘Shatangju’ mandarin grafted onto 5 rootstocks: Fragrant orange ( Citrus junons  Sieb. ex. Tanaka), Red tangerine ( Citrus reticulata  Blanco), ‘Shatangju’ mandarin ( Citrus reticulata  Blanco), Rough lemon ( Citrus jambhiri  Lush) and Canton lemon ( Citrus limonia  Osbeck). The tree size of ‘Shatangju’ mandarin grafted onto Canton lemon and Rough lemon were the largest, followed by self-rooted rootstock trees, and the lowest tree sizes correspond to ones grafted on Red tangerine and Fragrant orange rootstocks. The levels of indoleacetic acid (IAA) and gibberellin (GA) were significantly and positively related to growth vigor. The differences of gene expression in leaves of trees grafted onto Red tangerine, Canton lemon and ‘Shatangju’ mandarin were analyzed by RNA-Seq. Results showed that more differentially expressed genes involved in oxidoreductase function, hormonal signal transduction and the glycolytic pathway were enriched in ‘Red tangerine vs Canton lemon’. qRT-PCR analysis showed that expression levels of  ARF1 ,  ARF8 ,  GH3  and  IAA4  were negatively correlated with the growth vigor and IAA content. The metabolism of GA was influenced by the differential expression of  KO1  and  GA2OX1  in grafted trees. In addition, most of antioxidant enzyme genes were up-regulated in leaves of trees grafted onto Red tangerine, resulting in a higher peroxidase activity. We concluded that different rootstocks significantly affected the expression of genes involved in auxin signal transduction pathway and GA biosynthesis pathway in the grafted plants, and then regulated the hormone levels and their signal pathways.

Transcriptome Profiling to Understand the Effect of Citrus Rootstocks on the Growth of ‘Shatangju’ Mandarin