Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines

Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes Zfl1 and Zfl2, duplicate orthologs of Arabidopsis LEAFY, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of Zfl1 and Zfl2 from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of Zfl1 and Zfl2, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified Zfl1 into 16 haplotypes encoding 16 different proteins and Zfl2 into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the Zfl1 CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the Zfl2 locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the Zfl1 locus and 16 recombination events at the Zfl2 locus.