Patterns of genomic changes with crop domestication and breeding

Crop domestication and further breeding improvement have long been important areas of genetics and genomics studies. With the rapid advancing of next-generation sequencing (NGS) technologies, the amount of population genomics data has surged rapidly. Analyses of the mega genomics data have started to uncover a previously unknown pattern of genome-wide changes with crop domestication and breeding. Selection during domestication and breeding drastically reshaped crop genomes, which have ended up with regions of greatly reduced genetic diversity and apparent enrichment of potentially beneficial alleles located in both genic and non-genic regions. Increasing evidences suggest that epigenetic modifications also played an important role during domestication and breeding.