Abstract
Adaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range. To explicitly explore the demographic process underlying maize adaptation, we used a diffusion-based method to model the differentiation between temperate and tropical populations using the Non-Stiff Stalk group as a proxy for temperate maize. Based on multiple sequential Markovian coalescent approaches, we estimate that tropical and temperate maize diverged approximately 3‚000 to 5‚000 years ago and the population size shrank after the split. Using composite likelihood approaches, we identified a distinct tropical-temperate divergence event initiated 4‚958 years ago (95% confidence interval (CI): 4‚877–5‚039) from an ancestral population whose effective size was 24,162 (95% CI: 23,914–24,409). We found that continuous gene flow between tropical and temperate maize accompanied the differentiation of temperate maize. Long identical-by-descent tracts shared by tropical and temperate inbred lines have been identified, which might be the result of gene flow between tropical and temperate maize or artificial selection during domestication and crop improvement. Understanding the demographic history of maize diffusion not only provides evidence for population dynamics of maize, but will also assist the identification of regions under selection and the genetic basis of complex traits of agronomic importance.
Highlights
Adaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range
A total of 1.03 million high-quality single nucleotide polymorphisms (SNPs) generated from RNA sequencing of 368 maize inbred lines from Fu et al were kindly provided by Dr Fu16
We reconstructed the demographic history of the tropical-temperate split using the MSMC and the ∂a∂i approach
Summary
Adaptation to a temperate climate was a prerequisite for the spread of maize across a broad geographical range. Based on multiple sequential Markovian coalescent approaches, we estimate that tropical and temperate maize diverged approximately 3‚000 to 5‚000 years ago and the population size shrank after the split. We identified a distinct tropical-temperate divergence event initiated 4‚958 years ago (95% confidence interval (CI): 4‚877–5‚039) from an ancestral population whose effective size was 24,162 (95% CI: 23,914–24,409). Maize is a geographically widely distributed crop, grown from approximately 50°N to 45°S1 It originated from a single domestication event in southwestern Mexico[2], a tropical zone, more than 60% of maize is produced by countries that lie in the temperate zones[3]. Compared with the ABC method, ∂a∂i and MSMC are more efficient in handling high-throughput genomic data; we chose these two methods to estimate the demographic history of the tropical and temperate split in this study. Under many scenarios with little precognition of demographic history, MSMC analysis will provide evidence for demographic change and assist in constructing a more realistic model that can be used for other approaches that require a predefined model
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