Abstract
Crop improvement is a multifaceted micro-evolutionary process, involving changes in breeding approaches, planting configurations and consumption preferences of human beings. Recent research has started to identify the specific genes or genomic regions correlate to improved agronomic traits, however, an apparent blank between the genetic structure of crop elite varieties and their improving histories in diverse modern breeding programs is still in existence. Foxtail millet (Setaria italica) was one of the earliest cereal crops to be domesticated and served as a staple crop for early civilizations in China, where it is still widely grown today. In the present trial, a panel of foxtail millet elite varieties, which were released in the last sixty years in different geographical regions of China, was characterized using microsatellite markers (SSRs). A clear separation of two subpopulations corresponding to the two eco-geographical regions of foxtail millet production in China was identified by the dataset, which also indicated that in more recently released elite varieties, large quantities of accessions have been transferred from spring-sowing to summer-sowing ecotypes, likely as a result of breeding response to planting configurations. An association mapping study was conducted to identify loci controlling traits of major agronomic interest. Furthermore, selective sweeps involved in improvement of foxtail millet were identified as multi-diverse minor effect loci controlling different agronomic traits during the long-term improvement of elite varieties. Our results highlight the effect of transition of planting configuration and breeding preference on genetic evolvement of crop species.
Highlights
Genetic diversity of Chinese foxtail millet improved elite varieties All seventy-seven SSR markers were successfully amplified from DNA of all elite variety accessions, and all markers were polymorphic across the 348 accessions
The higher average allele number per locus observed in this study is likely the result of a larger sample size, covering a larger number of ecoregions and broader range of historical elite variety releases
Our previous study utilizing the same set of SSR markers identified an average of 20.9 alleles per locus in Chinese foxtail millet
Summary
Foxtail millet and its wild ancestor green foxtail (Setaria viridis) are currently being used to decipher the molecular basis of C4 photosynthesis, with the potential to create C4 rice with as much as a 50% yield increase [6] These same advantages allow foxtail millet to be used as a genetic model for closely related biofuels crops such as switch grass (Panicum virgatum) and napiergrass (Pennisetum purpureum), whose large polyploid genomes render traditional genetic and genomic approaches impractical [7,8]. We describe the population structure of a set of 348 elite varieties selected to be a representative sample of the diversity found across all the eco-regions of China in which foxtail millet is domesticated [21] and cultivated and to encompass the changes in population structure from the transition between landraces [14] to elite varieties as a result of changes in breeding and cultivation practices over the past 60 years. The marker data generated was employed to search for loci linked to variation in key agronomic traits using association mapping and to identify loci where diversity was reduced as a result of selection in the transition from landrace to elite varieties
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