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

Abstract

The domestication of maize has spanned a period of over 9000 years, 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 δ10 (Zm00001d045937), δ18 (Zm00001d037436), β15 (Zm00001d035760), γ16 (Zm00001d005793), γ27 (Zm00001d020592), and γ50 (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 z2δ18, whereas for z2β15 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 z2δ10 and z2γ50 had undergone natural selection. Indeed, a natural selection imprint could also be found with z2γ27 and z2γ16, whereas z2δ18 and z2β15 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.

Domestication of Crop Metabolomes: Desired and Unintended Consequences

“…This study revealed that evolutionary transitions in the levels of alkaloids, terpenoids, and lipids were targeted at the divergence between teosinte and tropical maize, whereas benzoxazinoids were targeted at the divergence between tropical and temperate maize. This study and another like it additionally examined either maize-teosinte cross populations or maize and teosinte populations separately, and identified candidate genes underlying differences in metabolite composition [90,91] or sulfur-rich storage proteins [97], respectively. The changes associated with domestication in rice, as compared to maize, were recently addressed in a metabolomic study [89], revealing that these species displayed different metabolomic shifts during their evolution, and moreover suggests that those shifts were different from those reported in wheat.…”

A 31-bp indel localised in the 5' untranslated region of OsSUT3 affects the gene expression and rice (Oryza sativa L.) pollen development

“…It is similar to the preservation of the 3-bp insertion in the promoter of the Sl-ALMT9 gene determined fruit malate contents and aluminium tolerance after tomato domestication (Ye et al 2017). Therefore, a positive selection pressure in evolution or domestication process often results in the reduction of genetic diversity, so the selection of polymorphism locus would be significant (Li et al 2018).…”

“…Indels, as the common MAS, were crucial prognostic factors af-fecting the gene expression and plant phenotype in molecular-assisted breeding. In maize, indels derived from teosintes (a maize ancestor) were selected to be reserved or discarded in different types of zein2 (z2) genes during domestication (Li et al 2018). In the sunflower, a 999-bp upstream insertion in the promoter region of the HaCYC2c gene resulted in a garden variety with disc floret bilaterality (Chapman et al 2012).…”

A natural single‐nucleotide polymorphism variant in sulfite reductase influences sulfur assimilation in maize

“…In the past few decades, maize breeders have taken great efforts to increase the nutritional quality of maize for humans and livestock to address this gap. A previous study has shown that a subset of sulfur‐rich zeins had undergone natural selection during maize domestication (Li et al ., 2018). Overall, although it may be difficult to evaluate the degree to which the positive selection on SNP69C contributed to adaptation during maize cultivation from tropical to temperate regions, we propose that the selection on SNP69C in ZmSiR may have facilitated the adaptation of maize growing in high‐altitude regions, which was likely beneficial for cold tolerance or nutritional biofortification.…”