Genetic diversity and evolution of reduced sulfur storage during domestication of maize

The domestication of maize has spanned a period of over 9000years, during which time its wild relative teosinte underwent natural and artificial selection. We hypothesize that environmental conditions could have played a major role in this process. One factor of environmental variation is soil composition, which includes sulfur availability. Sulfur is reduced during photosynthesis and is used to synthesize cysteine and methionine, which drive the accumulation of 10 (Zm00001d045937), 18 (Zm00001d037436), 15 (Zm00001d035760), 16 (Zm00001d005793), 27 (Zm00001d020592), and 50 (Zm00001d020591) zeins, representing the zein2 fraction (z2) of storage proteins in maize seeds. In this study, polymorphisms and haplotypes were detected based on six z2 genes in 60 maize and teosintes lines. Haplotypes were unevenly distributed, and abundant genetic diversity was found in teosintes. Polymorphism was highest in z218, whereas for z215 single nucleotide polymorphism (SNP) density and insertion/deletion (indel) abundance were the lowest, indicating differential roles in seed evolution. Indels showed a clustered distribution, and most of these derived from teosintes. The indels not only led to tandem repeat polymorphisms, but also to frameshift mutations, which could also be used as null variants. In addition, neutral evolutionary tests, phylogenetic analyses, and population structures indicated that z210 and z250 had undergone natural selection. Indeed, a natural selection imprint could also be found with z227 and z216, whereas z218 and z215 tended to be under neutral evolution. These results suggested that genetic diversity and evolution of a subset of sulfur-rich zeins could be under environmental adaptation during maize domestication.