Using a periclinal chimera to unravel layer‐specific gene expression in plants

Abstract

Plant organs are made from multiple cell types, and defining the expression level of a gene in any one cell or group of cells from a complex mixture is difficult. Dicotyledonous plants normally have three distinct layers of cells, L1, L2 and L3. Layer L1 is the single layer of cells making up the epidermis, layer L2 the single cell sub-epidermal layer and layer L3 constitutes the rest of the internal cells. Here we show how it is possible to harvest an organ and characterise the level of layer-specific expression by using a periclinal chimera that has its L1 layer from Solanum pennellii and its L2 and L3 layers from Solanum lycopersicum. This is possible by measuring the level of the frequency of species-specific transcripts. RNA-seq analysis enabled the genome-wide assessment of whether a gene is expressed in the L1 or L2/L3 layers. From 13 277 genes that are expressed in both the chimera and the parental lines and with at least one polymorphism between the parental alleles, we identified 382 genes that are preferentially expressed in L1 in contrast to 1159 genes in L2/L3. Gene ontology analysis shows that many genes preferentially expressed in L1 are involved in cutin and wax biosynthesis, whereas numerous genes that are preferentially expressed in L2/L3 tissue are associated with chloroplastic processes. These data indicate the use of such chimeras and provide detailed information on the level of layer-specific expression of genes.

A small indel mutation in an anthocyanin transporter causes variegated colouration of peach flowers

“…These three types of variegated flowers occur at low frequency, with no branches that produce predominantly one of the three types of variegated flowers. This is consistent with a previous finding that sectorial and mericlinal chimeras are unstable ( Pelsy, 2010 ; Filippis et al , 2013 ). In contrast, periclinal chimeras are very stable giving rise to the pink-flower branch that bears predominantly pink flowers.…”

“…The word chimera indicates that one or more layers consist of genetically distinct cells, and chimerascan be classified as periclinal, mericlinal, or sectorial chimeras. For floral meristems, layers L1 and L2 contribute to epidermis and internal tissues, respectively, while layer L3 forms the innermost tissues such as vascular tissues ( Brand et al , 2001 ; Filippis et al , 2013 ). Thus, layers L1 and L2 play an important role in determining flower colouration ( Stewart and Dermen, 1979 ; Carles and Fletcher, 2003 ).…”

The Tomato MIXTA-like Transcription Factor Coordinates Fruit Epidermis Conical Cell Development and Cuticular Lipid Biosynthesis and Assembly

“…In the SlMIXTA-RNAi lines, an ortholog to these genes, SlGL2 (Solyc03g120620), was shown to be down-regulated (Table II). The 93 down-regulated genes were also analyzed for their L1-layer specificity by comparison with a recently generated data set (Filippis et al, 2013). In this work, 255 of the 13,277 genes examined were identified to exhibit L1 layer-specific tomato expression.…”

Research Article Periclinal chimera technique: new plant breeding approach

“…It was found out that exchange of RNA and DNA to adjacent cells in grafts occurs (Hirata et al, 1999(Hirata et al, , 2000Stegemann and Bock, 2009;Nassar and Bomfim, 2013). In plant chimeras obtained by grafting, L1, L2, and L3 origins have also been identified by differential gene expression as well as the presence of different proteins in various histogenic-derived tissues (Filippis et al, 2013). Chimera 1 characterized by Nassar and Bomfim (2013) also gave significantly higher root yield as compared to its parent, UnB 201 (10-12 vs 2-3 kg/plant) but not reached this case.…”