Genetic Architecture of Domestication-Related Traits in Maize

Abstract

Strong directional selection occurred during the domestication of maize from its wild ancestor teosinte, reducing its genetic diversity, particularly at genes controlling domestication-related traits. Nevertheless, variability for some domestication-related traits is maintained in maize. The genetic basis of this could be sequence variation at the same key genes controlling maize-teosinte differentiation (due to lack of fixation or arising as new mutations after domestication), distinct loci with large effects, or polygenic background variation. Previous studies permit annotation of maize genome regions associated with the major differences between maize and teosinte or that exhibit population genetic signals of selection during either domestication or postdomestication improvement. Genome-wide association studies and genetic variance partitioning analyses were performed in two diverse maize inbred line panels to compare the phenotypic effects and variances of sequence polymorphisms in regions involved in domestication and improvement to the rest of the genome. Additive polygenic models explained most of the genotypic variation for domesticationrelated traits; no large-effect loci were detected for any trait. Most trait variance was associated with background genomic regions lacking previous evidence for involvement in domestication. Improvement sweep regions were associated with more trait variation than expected based on the proportion of the genome they represent. Selection during domestication eliminated large-effect genetic variants that would revert maize toward a teosinte type. Small-effect polygenic variants (enriched in the improvement sweep regions of the genome) are responsible for most of the standing variation for domestication-related traits in maize.KEYWORDS quantitative trait loci; nested association mapping; genome-wide association study; variance components; Zea mays T HE domestication of all major crop plants occurred in a relatively short period in human history, starting 10,000 years ago (Harlan 1992). During the domestication process, seeds of preferred forms were selected and saved to plant subsequent generations. Some alleles favored under domestication may have been neutral or even deleterious for the survival of wild plant species; for example, seed shattering promotes seed dispersal in wild grasses, but alleles for nondisarticulating seed structures were strongly selected for under domestication (Galinat 1983). Consequently, rare alleles favorable for growth and development under agricultural conditions or for traits desired by humans increased in frequency, often reaching fixation and reducing genetic variation very near causal sequence sites (Wang et al. 1999). In addition, domestication was often accompanied by severe genetic bottlenecks from the use of small founder populations. The reduction in effective population sizes also resulted in reduced genetic diversity genome-wide. Population genetics methods to model the strength and duration of bottlenecks provide a means to ...

Evolutionary and functional genomics of DNA methylation in maize domestication and improvement

“…The results were insignificant for 2nd and 3rd levels contacts (Figure S12A). We found 5/60 genes (Enrichment test P-value < 0.01) were domestication candidate genes as reported previously [51][52][53][54]. Two of them were Zm00001d018036 gene associated with cob length (P-value = 6 × 10 −25 ) and Zm00001d041948 gene associated with shank length (P-value = 5.6 × 10 −10 ) [51].…”

What can genome‐wide association studies tell us about the evolutionary forces maintaining genetic variation for quantitative traits?

“…Diversification traits can include analogs to those that might vary in wild populations, such as photoperiod sensitivity, but will also include characters that were consciously selected for by humans and may not have analogous natural variation, such as the popping phenotype in maize (Meyer & Purugganan, 2013). Because most GWAS panels focus on domesticated lines, diversification traits are the ones most likely to be investigated during plant GWAS, although there is evidence that when variation in domestication-related traits does persist in domesticated species, this variation is mainly due to small-effect alleles that escaped selection during domestication (Xue et al, 2016). It is unclear if conclusions made about variation in domestication traits or those diversification traits without analogs in natural populations will be applicable to questions about what maintains trait variation in nature.…”

Genomic history of the origin and domestication of common bean unveils its closest sister species

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