Abstract
Efficient recombination is critical to both plant breeding and gene cloning. However, almost all traditional recombination studies and genetic improvements require the slow and labor-intensive population construction process, and little is known about the recombination characteristics of populations of different types, generations, and origins. Here, we provide a simple and efficient simulation method for population construction based on doubled haploid (DH) and intermated B73 × Mo17 maize (IBM) populations to predict the recombination pattern. We found that the chromosomes had 0, 1, 2, and 3 recombination events that occurred at rates of 0.16, 0.30, 0.23, and 0.15, respectively, in the DH and the recombination rate of each chromosome in the IBM population ranged from 0 to 12.1 cM per 125 kb. Based on the observed recombination parameters, we estimated the number of recombination events and constructed the linkage maps of the simulated DH and recombination inbred line (RIL) populations. These simulated populations exhibited similar recombination patterns compared with the real populations, suggesting the feasibility of this simulation approach. We then compared the recombination rates of the simulated populations of different types (DH induced or self-crossed), generations, and origins (using the 8, 16, and 32 multiparent advanced generation intercross (MAGIC) populations), and suggested a rapid and cost-effective population construction procedure for breeders and geneticists, while maintaining an optimal recombination rate. This study offers a convenient method for optimizing the population construction process and has broader implications for other crop species, thereby facilitating future population studies and genetic improvement strategies.
Highlights
Recombination is the main driving force of genome evolution and genetic diversity [1]
Recombination pattern is mainly determined by two parameters—the number of recombination events per chromosome and recombination rate of each
The results showed that the estimated recombination rate of the 32-parent multiparent advanced generation intercross (MAGIC) population constructed by the doubled haploid (DH) method was comparable to that of the 16-parent MAGIC population generated by the CS strategy
Summary
Recombination is the main driving force of genome evolution and genetic diversity [1]. During this process, double-strand breaks (DSB) are generated during meiosis and crossover events are formed upon DNA repair. To facilitate crop breeding and gene cloning, several aspects of recombination need to be more well-understood, including the recombination patterns of different generations and populations [4]. Recombination pattern is known to vary significantly among different populations, including the doubled haploid (DH) population, recombination inbred lines (RILs), intermated B73 × Mo17 maize (IBM) population, and multiparent advanced generation intercross (MAGIC) population. Recombination studies have been previously performed in these populations, the influences of population types and generations on recombination patterns are largely unknown [5,6]
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