The Ge Laboratory, IBCAS

3. Origin and genetic diversity of the cultivated rice

It has been debated for a long time that when, where, and how the Asian cultivated rice originated. Based on the sequences of 10 nuclear genes, we found comparable levels of nucleotide variation between O. rufipogon and O. nivara, without significant genetic differentiation between them. Importantly, only 20-30% of the diversity in the wild species was retained in O. sativa, suggesting a severe bottleneck during rice domestication (Figure 3-1) (Zhu et al. 2007. MBE). Further molecular population analyses on two shattering loci (sh4 and qSH1) in Oryza sativa and its wild progenitors (O. nivara and O. rufipogon) indicated that the nonshattering sh4 allele had a single origin and selection on sh4 allele could be strong enough to have driven its fixation in a population of cultivated rice within a period of approximately 100 years; whereas no selection was detected for qSH1 (Zhang et al. 2009. New Phytol), providing new insights into the rate of rice domestication (Zhang et al. 2009. New Phytol).

Figure 3-1. Comparisons of nucleotide polymorphism of main crops, indicating a significant reduction of nucleotide diversity in cultivated rice relative to its wild progenitors.

Based on these observations and other lines of evidence, together with Tao Sang of Michigan State University, we proposed two models (combination and snowballing models) (Figure 3-2) to reconcile previously conflicting evidence regarding rice domestication (Sang & Ge. 2007 JIPB & Curr Opin Genet Dev).

Figure 3-2. Snowballing (a) and combination (b) models for rice domestication. Shapes (triangle, square, and circle) inside of cultivated rice represent important domestication genes fixed in all cultivars.

Despite extensive studies on cultivated rice, the genetic structure and subdivision of this crop remain unclear at both global and local scales. Using 84 nuclear simple sequence repeat markers, we genotyped a panel of 153 global rice cultivars covering all previously recognized groups and 826 cultivars representing the diversity of Chinese rice germplasm (Wang et al. 2014. Heredity). We confirmed the widely accepted five major groups of rice cultivars (indica, aus, aromatic, temperate japonica and tropical japonica), and demonstrated that rayada rice was unique in genealogy and should be treated as a new (the sixth) major group of rice germplasm (Figure 3-3). With reference to the global classification of rice cultivars, we identified three major groups (indica, temperate japonica and tropical japonica) in Chinese rice germplasm and observed that all seasonal, drought-tolerant and endosperm types occurred within each of three major groups, which does not support previous claims that seasonal differentiation exists in Indica and drought-tolerant differentiation is present in Japonica. It is most likely that differentiation of cultivar types arose multiple times stemming from artificial selection for adaptation to local environments.

Figure 3-3. Population genetic structure of Asian cultivated rice. (A) NJ tree of 153 global rice accessions; (B) NJ tree of the combined 153 global and 826 Chinese accessions.

The question of origin and domestication of cultivated plants is a hot topic in biological research. In the rice genus, two cultivated species, Asian rice (Oryza sativa L.) and African rice (O. glaberrima Steud.), were domesticated independently in Asia and Africa. However, whether a single or multiple origins for either of them continues debated. We used 14 unlinked nuclear genes to investigate the origin and domestication history of African rice (Li et al. 2011. TAG). Population and genealogical analyses both support a single origin of African rice in areas of the Upper Niger and Sahelian Rivers. Moreover, coalescent simulation indicated a double evolutionary during the domestication of African rice, i.e., the first was associated with the divergence of its ancestor (O. barthii) from Asian Oryza species and the second happened during its domestication from the initial populations of O. barthii in Africa.

Figure 3-4. Phylogenetic analysis showed a single domestication origin of African cultivated rice (Oryza glaberrima). Blue (square) and red (triangle) dots represent the cultivated O. glaberrima and its closely related wild species O. barthii, respectively.