The Virgin with the Infant Saint John the Baptist adoring the Christ Child accompanied by an Angel ('The Virgin of the Rocks')

This is one of Leonardo's most mysterious and complex pictures. It's a rare survival of one of his large-scale painted works, and a key example of many of the techniques and innovations with which he transformed Italian painting. Leonardo began his painting career in Florence, but in the early 1480s he offered his services to Milan's ruling family, the Sforzas. While in Milan, he received the commission to paint 'The Virgin of the Rocks'.

The painting was to be part of a grand altarpiece which included a large sculpture of the Virgin Mary, probably placed above it. The chapel that the altarpiece was destined for was in the church of San Francesco Grande, a Franciscan convent in Milan. The chapel belonged to the newly-formed confraternity of the Immaculate Conception of the Virgin Mary and it was dedicated to this feast.

The notion of the Immaculate Conception, which emerged in the twelfth century, was highly controversial but championed by the Franciscans. The idea was important because in order for Christ to be born without original sin (which passed from Adam and Eve for disobeying God), his mother, Mary, also had to be free of sin. The doctrine's supporters argued that the Virgin had been conceived by God even before the creation of the world - and so before original sin.

Leonardo's painting was commissioned shortly after the pope officially sanctioned celebration of the feast in 1477. The subject was still so new that there was no standard way of showing it, giving Leonardo free rein to create a new composition. He painted the Virgin, an infant Saint John the Baptist - a gilded cross under his arm - and an angel, kneeling around Christ, a chubby cross-legged child. The three figures communicate with each other in silence while the angel acts as a heavenly witness to the scene. They are embedded in the landscape: foliage tickles Saint John's knees and Christ's toes, and rocks hem them in on all sides.

Writers who supported the Immaculate Conception defended their argument using biblical passages that expressed the pre-existence of divine Wisdom (later associated with the Virgin). One of these was a verse in which Wisdom says: 'From the beginning and before the world, was I created, and unto the world to come I shall not cease to be' (Ecclesiasticus 24:14). This might explain why Leonardo has placed the figures in a shady grotto, with views through the rocks to a watery landscape beyond. These primitive elements suggest the scene is set in the earliest moments of creation: the first verses of the biblical creation story tell of God creating the earth out of the watery deep. The rocks are shaped like rounded cones - they look as though they have just emerged from the depths of the earth, like volcanic eruptions. Their upward energy contrasts with the water's stillness, the green of which suggests it is shallow, like a swamp. A haze over the water suggests its warmth - a fetid pool, ripe with the promise of life. The place is certainly fertile: the plants around Saint John the Baptist's knees are firm and luscious, the leaves plump. Plants even sprout from the rocks above; the landscape is alive.

In this picture we see examples of many of Leonardo's broad range of interests. His surviving drawings include numerous studies of nature: dramatic rock formations, trees and detailed plant studies. He was fascinated by the power of the natural world; he made nine drawings of an imaginary deluge, expressing the force of water. He paints the rocks of the holy grotto with immense attention to the detail of their texture; we can almost feel it ourselves under the infant Christ's left hand. But the flowers don't resemble any real flowers - they're hybrids of different plants.

Leonardo has used his inventive technique, now called aerial perspective, to give the impression of a vast landscape setting. He realised that we perceive the same colours differently depending on their distance from us; green appears blue if viewed from far off. By painting the mountains in the background blue, he tricks us into believing they are in the far distance. He softened their edges so they appear hazy, another technique that mimics the effects of vision in reality. The cool blue-green also contrasts directly with the rich, warm red-brown of the earth.

The figures emerge softly from the darkness of the grotto. Leonardo created this effect by painting very subtle, rather than stark, transitions between light and dark. This created a blurry effect around the edges of forms - look at the Virgin's temples and nose for example - a technique later called sfumato. As with 'aerial perspective', this idea was a result of his experiments into vision and perception in this period. Leonardo built up his figures using layers of black and white underpainting, showing his knowledge of the way we perceive shapes through the effect of light and shadow on their surfaces.

Recent conservation work has revealed that Leonardo painted this, his second version of the picture, in three phases. He probably started in the early 1490s, painting the angel's delicate gauze sleeve. Technical examination shows that a few years later he changed the position of Christ's head, turning it from a three-quarter to profile view. In 1499 he left Milan for Florence to escape the turbulence caused by the French invasion of the city. He was summoned to return to finish the picture in 1506, when he added a layer of ultramarine (an expensive blue pigment) to the sky - as specifically mentioned in the original contract.

Our panel, begun about a decade after the first version, has been painted in a significantly different style. Some areas appear to be unfinished if viewed up close, but this was probably deliberate: it enables us to focus on the most important features. There are fewer colours too - it is mainly blue, yellow and brown. Leonardo has changed the angel's robes from red to blue, probably to simplify the picture and focus attention on the Virgin's yellow draperies.

Credit: Bought, 1880