Genes Contributing to Domestication of Rice Seed Traits and Its Global Expansion

Abstract

Asian rice (Oryza sativa) and African rice (Oryza glaberrima) are separately domesticated from their wild ancestors Oryza rufipogon and Oryza barthii, which are very sensitive to daylength. In the process of domestication, some traits that are favorable for the natural survival of wild rice such as seed dormancy and shattering have become favorable ones for human consumption due to the loss-of-function mutations in the genes that are underlying these traits. As a consequence, many genes that are related to these kinds of traits have been fixed with favorable alleles in modern cultivars by artificial selection. After domestication, Oryza sativa cultivars gradually spread to temperate and cool regions from the tropics and subtropics due to the loss of their photoperiod sensitivity. In this paper, we review the characteristics of domestication-related seed traits and heading dates in rice, including the key genes controlling these traits, the differences in allelic diversity between wild rice and cultivars, the geographic distribution of alleles, and the regulatory pathways of these traits. A comprehensive comparison shows that these genes contributed to rice domestication and its global expansion. In addition, these traits have also experienced parallel evolution by artificial selection on the homologues of key genes in other cereals.

Keywords: domestication; flowering time; global expansion; parallel evolution; seed dormancy; seed shattering.

Figure 1

The regulatory network of rice flowering. Lines with a triangle indicate active transcriptional regulation; lines with a cap indicate a repression of transcriptional regulation; lines with a dot indicate phosphorylation; dotted lines indicate genetic interaction; and the dark background indicates that Hd1 interacts with Ghd8 and Ghd7 to largely repress Ehd1 and Hd3a/RFT1 expression.

Figure 2

Two-step selection from wild rice to modern cultivars.