The hormonal control of fruit growth and development has been well established across many different plants. One hormone, auxin, has been shown to control the initial growth and expansion of tissues following fertilisation [1, 2] and inhibit ripening. Early work with strawberry and other fruits proposed a mechanism whereby auxin produced by the developing seed regulated fruit growth by controlling firstly cell division and secondly cell expansion. As the seeds subsequently mature, auxin concentrations drop, acting as a signal for ripening to proceed. Supporting this mechanism is the observation that applied auxins can induce parthenocarpy in fruits such as tomato , fruit size in peach , cell enlargement in cherry  and delay ripening in strawberry . Developmental regulation by the principal auxin in higher plants, IAA (Indole Acetic Acid), is achieved through the coordination of complex processes: auxin metabolism (involving biosynthesis, conjugation and catabolism), auxin transport (long distance and polarised auxin transport) and auxin signalling (perception, transduction and response). The balance of synthesis, breakdown, conjugation and transport is tightly regulated, leading to auxin homeostasis .
De novo auxin synthesis in plants results from multiple pathways dependent or independent of tryptophan [7, 8]. IAA can be conjugated to amino acids, sugars and methyl esters. Enzymes that conjugate IAA to amino acids are encoded by members of the group II of the GH3 (Gretchen Hagen 3) family of auxin-induced genes . Very little is known about the role of GH3 genes during fruit development. However, it has recently been shown in grape that GH3.1 plays a role in the formation of IAA-Asp late during development, coinciding with the onset of ripening . Release of IAA from IAA conjugates is achieved by hydrolytic cleavage . Auxin transport from sites of synthesis to target cells is complex and highly regulated, playing a crucial role in both establishing and changing homeostasis. Auxin is transported both passively through the vasculature and actively through transporters . The most characterised auxin transport family is the efflux carrier PIN family. PIN proteins are vital for normal plant development. Mutations in the PIN1 gene lead to pin-like organs with no development of flower parts in Arabidopsis thaliana (Arabidopsis)  and members of the PIN family are highly expressed early during tomato fruit development, suggesting a role during fruit set .
The current model for auxin perception and signalling involves two types of receptors [15, 16]: the Auxin Binding Protein 1 (ABP1), located at the plasma membrane, and the Transport Inhibitor 1/Auxin signalling F-Box family (TIR1/AFB), a set of nuclear receptors [17–19]. ABP1 is involved in very early auxin responses leading, for example, to the modification of ion fluxes . ABP1 has been shown to be essential for plant life (a mutation in ABP1 in Arabidopsis is lethal) and is important for both cell division and cell expansion [21–23]. However, the details of the pathway going through ABP1 are poorly understood. In tomato, the diageotropica (dgt) mutant displays many auxin-related developmental defects and fruit development is dramatically altered, with a reduced fruit size . DGT encodes a cyclophilin, known to act as signalling intermediate, and was shown to use ABP1 as an extracellular receptor for auxin-dependent cell growth response . The signalling pathway involving TIR1 is now well characterised and explains most of auxin-regulated gene expression . The three families of early auxin responsive genes, Aux/IAA, GH3 and SAUR (Small Auxin Up Regulated), contain a binding motif to the ARF transcription factor (Auxin Response Factor). At low auxin concentrations, a heterodimer of an ARF and an Aux/IAA protein represses transcription. At higher auxin concentration, auxin will bind to TIR1/AFB, an F-box protein that is part of an SCF complex (Skp1/Cullin/F-box), and triggers the degradation of the repressor Aux/IAA through the 26S proteasome. This will ultimately release the ARF transcription factor to modulate expression of early auxin response genes. In fleshy fruits, most of our knowledge involving the ARF-Aux/IAA complex during fruit development comes from studies in tomato. SlARF7 is expressed in placental and ovule tissues and down-regulated soon after pollination. Silencing of the SlARF7 gene leads to parthenocarpic fruit development, showing that SlARF7 functions as a negative regulator of fruit set . Similarly, silencing of the SlIAA9 gene expression also confers parthenocarpy . SlARF4 (also known as DR12) seems to play a role later in fruit development, as its expression increases throughout tomato fruit development, with the highest levels in early red-stage fruit. Down-regulation of SlARF4 leads to pleiotropic phenotypes including dark-green immature fruit, enhanced firmness and unusual cell division in the fruit pericarp, which is thicker than in wild-type (WT) fruits [28, 29].
While many fleshy fruits are carpel derived, the fruit from Malus x domestica (apple) is unusual, as it is derived from the hypanthium, a tube of fused sepals, petals and anther derived tissue. However, like other fruits, apple development can be separated into periods of cell division, cell expansion, maturity, and ripening . While there have been a few studies on auxin content in apple [31, 32], there is little research reported on the role of auxin in apple fruit development at the molecular level. There are a large number of different cultivars of apples showing a range of different flowering times, maturity times and times to ripen. One cultivar, 'Royal Gala', is a naturally occurring sport of the 'Gala' cultivar. It is a mid-season apple, and its growth and development has been well characterised. 'Royal Gala' has been the subject of a number of genomics studies, including a large-scale expressed sequencing tag (EST) sequencing project  and a microarray study of the fruit development  and fruit ripening . It is readily transformable, with transgenic apples for ACO1 suppression [34, 35], MYB10 overexpression , and POLYGALACTURONASE 1  being reported. Recently a parent of 'Royal Gala', 'Golden Delicious', has had its genome sequenced .
Here we have investigated the role of auxin on apple fruit development and assessed the expression of genes involved in homeostasis, transport and signalling of auxin. The location of auxin-related genes in the genome sequence of apple was compared with QTLs for fruit weight, which is linked to fruit size.