Figure 1.

Domestication genes and domestication processes. Circles with blue and orange backgrounds represent independently domesticated cultivars of a crop. Double arrowheads indicate gene flow between them during the process of domestication. A, Red triangle in the top blue circle represents the single origin of a domestication allele. The beneficial allele is subsequently fixed in this cultivar and spreads and also becomes fixed in the other cultivar. Examples for this scenario include nud in barley and sh4 in rice if qSH1 was derived in some japonica cultivars after the fixation of sh4 (see text for explanation). B, Black triangle in the top orange circle represents the independent origin of another allele at the same locus as the red triangle. Two alleles (red and black) have the similar function and coexist in the modern cultivars. Examples for this scenario include the loss-of-function alleles of Vrs1 in barley and Sc in rice. C, Alleles at two different loci, represented by a red triangle and a black square, are selected during the independent domestications. The red allele is more beneficial than the black allele and there is negative epistasis between them. Artificial selection fixes the red gene in both cultivars with only a small portion of the orange cultivar still retaining the black gene. The example may include the coexistence of sh4 and qSH1 in some japonica cultivars in the case that qSH1 originated in japonica before the introgression of sh4. D, In the case of two domestication loci being initially selected, if the red gene is more beneficial than the black gene and/or there is a negative epistasis between them, the black gene is eliminated from the cultivars and the red gene ends up being the only domestication gene fixed in the modern cultivars. This is a more generalized case for scenario A assuming that there had been another gene targeted by artificial selection at the initial stage of domesticating the orange cultivar.