Comparative Genetics Of Domestication In Foxtail Millet and Other Grasses

Genetic control of three traits (shattering, branching, and flowering time) that represent different aspects of moving wild plants into domestication were examined in foxtail millet (Setaria italica).  Selection of non-shattering seed is likely an early event in all cereal domestications, whereas selection on vegetative branching and flowering time are likely later events in crop improvement. In foxtail millet we find quantitative trait loci (QTL) regions for shattering that are likely the result of at least two novel mutations (one of which has been reported from foxtail millet, sorghum, rice and maize, Lin et al. 2012).  For vegetative branching we find a mixture of likely candidate genes from other grasses as well as novel regions.  In addition we find a large degree of genotype by environment interaction for many QTL regions.  For flowering time we find that most genes underlying QTL regions are from conserved flowering time pathways in the grasses, and, in addition, flowering time QTL are stable over a range of photoperiod regimes.  Comparative genomic analysis suggests that genetic changes responsible for the early stages of cereal domestication are more likely to be novel mutations, whereas in the improvement stage, selection can either be on standing variation for conserved pathways or on novel mutations in specific lineages.