Identification and Characterization of miRNAs in Self-Rooted and Grafted Malus Reveals Critical Networks Associated with Flowering

Abstract

Grafting can improve the agricultural traits of crop plants, especially fruit trees. However, the regulatory networks and differentially expressed microRNAs (miRNAs) related to grafting in apple remain unclear. Herein, we conducted high-throughput sequencing and identified differentially expressed miRNAs among self-rooted Fuji, self-rooted M9, and grafted Fuji/M9. We analyzed the flowering rate, leaf morphology, and nutrient and carbohydrate contents in the three materials. The flowering rate, element and carbohydrate contents, and expression levels of flowering genes were higher in Fuji/M9 than in Fuji. We detected 206 known miRNAs and 976 novel miRNAs in the three materials, and identified those that were up- or downregulated in response to grafting. miR156 was most abundant in Fuji, followed by Fuji/M9, and then self-rooted M9, while miR172 was most abundant in M9, followed by Fuji/M9, and then Fuji. These expression patterns suggest that that these miRNAs were related to grafting. A Gene Ontology (GO) analysis showed that the differentially expressed miRNAs controlled genes involved in various biological processes, including cellular biosynthesis and metabolism. The expression of differentially expressed miRNAs and flowering-related genes was verified by qRT-PCR. Altogether, this comprehensive analysis of miRNAs related to grafting provides valuable information for breeding and grafting of apple and other fruit trees.

Mechanisms Underlying Graft Union Formation and Rootstock Scion Interaction in Horticultural Plants

“…These outcomes are valuable for the purposeful analysis of miRNAs in the facilitation of grafting induced drought tolerance. An et al (2018) conducted a Gene Ontology study which showed that miRNAs which are expressed differentially throughout grafting regulated genes involved in a number of processes, including biosynthesis of cellular compounds and metabolism. Various studies revealed that miRNA172 can travel from source to sink in Nicotiana ( Kasai et al, 2010 ) and that miRNA156 functions as a signal which is mobile through the phloem to affect important traits in potato ( Bhogale et al, 2014 ).…”

Transcription Factor CsWIN1 Regulates Pericarp Wax Biosynthesis in Cucumber Grafted on Pumpkin

“…Grafting is an important way to improve plant growth, stress tolerance, and fruit quality, and has been widely used in commercial horticultural crop production (Zahaf et al, 2012; Liu et al, 2016). The molecular mechanisms regulating plant growth via grafting have been investigated by several groups (Kyriacou et al, 2017), for example using high-throughput sequencing in watermelon (Liu et al, 2013), tomato (Estan et al, 2005), apple (An et al, 2018), and grapevine (Pagliarani et al, 2017). These studies showed that grafting affects differential expression of genes in grafted plants.…”

Epigenetic Changes and Transcriptional Reprogramming Upon Woody Plant Grafting for Crop Sustainability in a Changing Environment

“…Although the two varieties were both grafted to the same rootstock, the relationship of grafting to the differential expression of the HMs was not investigated. An et al (2018) studied the miRNA expression in self-rooted and grafted Fuji apple trees by high-throughput sequencing in relation to flowering rate. Some of them that were differentially regulated in response to grafting (miR156, miR172, miR159, miR171) target genes encoding transcription factors that regulate flower formation, and suggested that there is a regulatory network between miRNAs and mRNAs that is generated by grafting.…”

“…mRNAs, miRNAs, and proteins can act as potential short- and long-distance signals exerting a regulatory role in the receiving graft partner which impacts scion but also whole plant performance. In grapevine, apple and avocado, miRNA and mRNA molecules as well as induction of transcriptional reprogramming in scions has been associated with physiological and metabolic pathways affecting traits of agronomical relevance ( Cookson et al, 2014 ; Kaja et al, 2015 ; Corso et al, 2016 ; Li et al, 2016 ; Chitarra et al, 2017 ; Pagliarani et al, 2017 ; An et al, 2018 ). Gaining a deeper insight into the molecular mechanisms underlying these processes could direct the development of suitable molecular markers to be used for generating and selecting superior grafts with improved yield, quality, and tolerance to abiotic and biotic stresses.…”