Genomic resequencing reveals the genetic diversity of the cultivated water caltrop,and the origin and domestication of'Nanhuling'
Aims:Understanding the origins and domestication processes of cultivated crops,is crucial for understanding human civilization.Trapa,commonly known as water caltrop,belongs to the family Lythraceae and is an annual floating-leaf aquatic herb.As a traditional aquatic vegetable crop,the fruit of Trapa has long been a significant food source in early Chinese agricultural societies.However,in recent years,rapid urbanization in China has resulted in habitat destruction,posing a serious threat to its genetic diversity.Moreover,'Nanhuling',a major cultivar of Trapa,holds high economic and cultural value,yet its origin and domestication history are not fully understood.Methods:In this study,we employed population genomics to investigate the genetic diversity of cultivated water caltrop and the domestication history of'Nanhuling'.The dataset for this study was generated by whole-genome resequencing of 31 diploid cultivated T.natans and 23 diploid wild T.natans samples.Results:Population genetic structure and differentiation indicated that wild and cultivated T.natans belonged to distinct gene pools.Cultivated T.natans originated from the diploid wild T.natans in the Yangtze River Basin.The overall genetic diversity level of cultivated T natans is lower than that of wild T.natans(0.68 × 10-3 vs.1.35 × 10-3),and the effective population size is significantly reduced compared to wild T.natans(～4,000 vs.～7,700),suggesting that cultivated T.natans experienced a genetic bottleneck during domestication.Among cultivated T.natans,'Nanhuling'exhibited the lowest level of genetic diversity and the slowest decay rate of linkage disequilibrium,which may be related to its high degree of domestication and strong selection pressure.Based on the population dynamic history inferred from the FASTSIMCOAL2 ancestral simulation model,we found that there had been gene flow events among'Nanhuling','Wuling',and other cultivated T.natans.The domestication of'Nanhuling'occurred approximately 669 years ago,consistent with literary records from the Ming Dynasty.Conclusions:This study is significant as it deepens our understanding of the domestication and genetic evolution of cultivated T.natans.Insights gained from this work may help improve agriculturally valuable characteristics of T.natans,such as crop yields and nutrient content.
origin and domesticationwater caltroporphan cropsaquatic plantsgenome resequencing
NETL
NSTL
万方数据
