Investigation of the bottleneck leading to the domestication of maize

Abstract

Maize (Zea mays ssp. mays) is genetically diverse, yet it is also morphologically distinct from its wild relatives. These two observations are somewhat contradictory: the first observation is consistent with a large historical population size for maize, but the latter observation is consistent with strong, diversity-limiting selection during maize domestication. In this study, we sampled sequence diversity, coupled with simulations of the coalescent process, to study the dynamics of a population bottleneck during the domestication of maize. To do this, we determined the DNA sequence of a 1,400-bp region of the Adh1 locus from 19 individuals representing maize, its presumed progenitor (Z. mays ssp. parviglumis), and a more distant relative (Zea luxurians). The sequence data were used to guide coalescent simulations of population bottlenecks associated with domestication. Our study confirms high genetic diversity in maize-maize contains 75% of the variation found in its progenitor and is more diverse than its wild relative, Z. luxurians-but it also suggests that sequence diversity in maize can be explained by a bottleneck of short duration and very small size. For example, the breadth of genetic diversity in maize is consistent with a founding population of only 20 individuals when the domestication event is 10 generations in length.

Figure 1

Schematic representation of the coalescent models used in simulation. See text for details.

Figure 2

The neighbor-joining reconstruction of Adh1 sequences. Bootstrap values greater than 50% are given above nodes. Abbreviations are given in Table 1.

Figure 3

Results of simulations based on model 1 and model 2. The right-hand y-axis of both graphs represents the population size N; N is calculated from θ assuming a mutation rate of 6.5 × 10⁻⁹ mutations per nucleotide site per year (29) over 997 nucleotide sites. For each graph, the top three lines represent estimates of θ_B based on different parameter values for d and θ_P. For ease of presentation, symbols are removed where lines overlap. The lowest plotted line represents estimates of lower 95% confidence of θ_B for θ_P = 24.3. This last line was nearly indistinguishable from lower 95% confidence intervals estimated with θ_P = 243 and θ_P = 2.43.