Writing recently in Plant Physiology, Sang Tao (who has done important work on finding and sequencing the sh4 domestication genes [Science 2006] which contributes to non shattering in domesticated rices-- and is shared across indica and japonica), reviews genes and mutations underlying domestication in grasses. It summarizes some of the recent functional genes reported and sequenced from rice, barley and wheat, with focus on thise genes involved in tough-rachis/ non-shattering. References to the archaeological record are absent. The general conclusion is that most domestication genes are a single mutation for a single trait, despite the fact that they are shared across diverse cultivated lines that may have different phylogenetic origins. He therefore conludes that hybridization and gene flow moved adaptive domestication genes across early cultivated populations. Indeed, this was probably a key factor in rice domestication. But contrary to Sang's assumption that non-shattering (sh4) arose in indica, I have argued (in a recent WA) it is likely to have arisen in japonica and spread to South Asia with japonica rice and other Chinese crops (and harvest knives) in the Late Harappan era (ca. 1900 BC), which represents something of a 'Chinese horizon' in northwestern South Asia.
There is a fundamental implication of a key role of hybridization in the formation of the crops we know today. Wheat researchers have long knwon this, due to polyploidy. Hexaploid bread did arise by hybridization, between a domesticated tetraploid and a wild relative. But genetics is increaaing suggesting this sort of thing was not the exception but the norm. Barley has tow distinct origins (West and East of the fertile crescent), but naked barleys of both origin share the mutation nud. The evidence indica rice clearly implicates hybridization in the making of fully domesticated indica: domestication genes that were selected by Neolithic Chinese farmers foufound their way through pollen into primitive prototype indica cultivars, which already had important adaptations to the monsoonal environment of South Asia.
This seems to raise a further question which is to what extent gene flow and hyrbdization was crucial in the earliest stages of pre-domestication cultivation? The move to accepting a protracted transition to domestication, would seem to open up this possiblility. Thus selection for large grains in one area, non-shattering in another, and erect growth in yet another seems plausible, and the extended period of pre-domestication cultivation may be necessary for this various adaptation to be brought together. Culturally this implies contact, the exchange and sharing seed stocks between communities, and in the case of rice apparently over long distances. For archaeologists who have studies things like the trade in obsidian, or the translocation of crops between African and India, in prehistory, this should come as no surprise. People were connected (even if irregularly and indirectly) over quite long distances sometimes. The evolution of cultivation systems and the crops in them was taking place in the context of interconnected communities and cultures.
Sang also raises but does not attempt the solve the historical problem that temperate japonica rices have another additional non-shattering gene (qsh1), which seems to me to be most likely selected for later as japonica cultivars were subjected to new forms of harvesting (such as basal harvesting by true sickles, which occur in China from the late 4th/ early third M. BC?) and processing.