Domestication of Rice

Oryza sativa as it exists today underwent domestication by a series of occurrences of hybridization and introgression between ancient gene pools and inbred lines (Kovach et al., 2007) . 13 domestication traits were associated with 76 QTLs (Lai et al., 2003), some of the genes that contribute to these traits are BH4 for seed pigment, SH4-1 and qSH1 for seed shattering, SD1 for dwarfism and BADH2 for fragrance (Meyer and Purugganan, 2013). One of the most important case studies is the elimination of seed shattering in rice, which consists of retaining the seeds on the straws to facilitate harvest and increase production yield (fig. 1). Wild rice (O. rufipogon Griff.) was domesticated to O. sativa and the genes shattering4 and qSH1, responsible for the abscission layer formation, were selected a non-shattering allele for them (Kovach et al., 2007). The shattering QTL, qSH1, was identified from an intra-specific japonica x indica cross (Konishi et al., 2006). Studies show that a SNP can cause a single amino acid change to regulate shattering through a transcriptional regulator as MyB3, for SH4, and a SNP in a regulatory region using homeodomain as a transcriptional regulator for qSH1. These SNP decrease the expression of the transcription factor responsible for abscission layer formation, dissolving the bonds between the cells that separates the grain from the plant, resulting in less shattering (Doebley et al., 2006; Kovach et al., 2007).

Figure 1- Wild rice on the left has a panicle that shatters, opposed to the domesticated rice on the right, which has a solid panicle of grain. From Doebley et al. (2006)

A consequence of this change was the dependence of humans for dispersion of their seeds (Fuller, 2007).

Bibliography

Doebley, J., Gaut, B. and Smith, B. (2006). The Molecular Genetics of Crop Domestication. Cell, 127(7), pp.1309-1321.

Fuller, D. (2007). Contrasting Patterns in Crop Domestication and Domestication Rates: Recent Archaeobotanical Insights from the Old World. Annals of Botany, 100(5), pp.903-924.

Konishi, S., Izawa, T., Lin, S., Ebana, K., Fukuta, Y., Sasaki, T. and Yano, M. (2006). An SNP Caused Loss of Seed Shattering During Rice Domestication. Science, 312(5778), pp.1392-1396.

Kovach, M., Sweeney, M. and McCouch, S. (2007). New insights into the history of rice domestication. Trends in Genetics, 23(11), pp.578-587. 

Lai, X., Hinga, M., Lobos, K., Martinez, C., McCouch, S., Thomson, M., Tai, T., McClung, A. and Xu, Y. (2003). Mapping quantitative trait loci for yield, yield components and morphological traits in an advanced 12 backcross population between Oryza rufipogon and the Oryza sativa cultivar Jefferson. TAG Theoretical and Applied Genetics, 107(3), pp.479-493.

Meyer, R. and Purugganan, M. (2013). Evolution of crop species: genetics of domestication and diversification. Nature Reviews Genetics, 14(12), pp.840-852.