Population Genetics Of Zizania Latifolia Based On Genomic Resequencing

The population genetic structure and evolutionary history of cultivated plants and their wild relatives（ancestors）has always been a hot research topic for biologists.Zizania latifolia is a widely distributed and valuable aquatic herb in China,and its cultivated type,Jiaobai,is the second largest aquatic vegetable in China.In recent years,many studies on Z.latifolia and Jiaobai based on microsatellite markers have failed to deeply reveal the genetic diversity and population dynamics history of Z.latifolia,as well as the domestication history of Jiaobai.With the development of sequencing technology and the publication of high-quality genome of Z.latifolia,it is necessary to carry out population genetics studies on Z.latifolia at the genomic level.In this study,172 individuals from43 populations of wild Z.latifolia and 28 different varieties of Jiaobai were collected extensively in China,and their genomes were resequenced,and compared with the genome of Z.latifolia to obtain a large number of molecular markers to explore the genetic variation and population dynamics history of Z.latifolia,the domestication origin of Jiaobai and the genes subject to selection.The main findings are as follows:（1）A total of 1610.03Gb resequencing data was obtained,with an average sequencing depth of 13.7×.After variant detection and filtering,a total of 3695324 single nucleotide polymorphism（SNP）sites were obtained for subsequent analysis.Phylogenetic analysis,principal component analysis and kinship structure analysis all showed that the 200 samples were divided into three genetic groups,the northern genetic group NOR,the southern genetic group SOU and the cultivated genetic group CUL.However,24 samples of wild Z.latifolia clustered into CUL,most likely as cultivated escaped individuals.The affinity of CUL was closer to the populations in the Taihu Lake Basin in SOU.The Pi values of nucleotide polymorphisms of NOR,SOU and CUL were1.80×10^-3,1.74×10^-3 and 1.40×10^-3,respectively.The F_ST values of genetic differentiation coefficients between NOR and CUL and between SOU and CUL were 0.25 and 0.20,respectively,while the F_ST value between NOR and SOU was 0.08.The Pi value of the wild genetic group WILD,which was formed by merging NOR and SOU,was 1.87×10^-3,and the F_ST value between WILD and CUL was 0.22.（2）Two different methods were used to detect population divergence between WILD and CUL,and 405 and 814 candidate genes,which were selected during artificial domestication of Jiaobai,were extracted,respectively.The enrichment analysis revealed that the significant enrichment pathways of these genes were concentrated in plant hormone metabolism and plant immune defense.Four different methods were used to comprehensively compare the NOR and SOU genetic groups to extract 164 candidate genes for adaptive evolutionary selection in wild Z.latifolia.The enrichment analysis revealed that these genes were significantly enriched in ribosomal pathway and diterpene biosynthesis pathway.（3）The historical analysis of population dynamics showed that the effective population size of SOU and NOR declined to different degrees 10,000 years ago.The maximum entropy model showed that wild Z.latifolia had a wider distribution in the northern part of China during the last glacial age than at present,and the bioclimatic factor with the highest contribution rate to both simulations was precipitation in the wettest month.The above results indicate that the genetic differentiation within the wild population of Z.latifolia is relatively low,while there is a high genetic differentiation between wild Z.latifolia and Jiaobai,which is likely caused by artificial domestication pressure in Jiaobai.Jiaobai has high genetic diversity and weak domestication bottleneck,and it likely originated from a single domestication in the Taihu Lake Basin.This study revealed the genetic diversity,genetic structure and population dynamics history of Z.latifolia and the domestication history of Jiaobai from the genomic level,and extracted candidate genes for adaptive evolution of Z.latifolia and domestication of Jiaobai,which also provided important genetic information resources for the exploitation of Z.latifolia germplasm and the domestication of Jiaobai in the future.