| Oryza rufipogon Griff.(RUF)belongs to family Poaceae.It is widely distributed in the south of China,and is a national second-class protected plant in taxonomy.It has the same AA genome as cultivated rice,and it is widely recognized as the ancestor of Asian cultivated rice.At present,cultivated rice in the world is facing a crisis of narrow genetic basis,and ordinary wild rice has become an important source for widening the genetic basis of cultivated rice due to its special genetic relationship and rich genetic diversity.However,with the rapid population growth,environmental pollution,water conservancy,urban construction,and alien species intrusion have made the population of O.rufipogon on the brink of extinction.Earlier research on O.rufipogon populations only stayed at the research level of small data such as phenotypic observation and microsatellite analysis,but key issues such as population genetic characteristics and special environmental adaptation mechanisms of RUF have not been better solved.In this paper,we constructed a genome-wide genetic variation map of RUF,and revealed it’s genetic structure at genome-wide level.We also systematically analyzed and compared genetic coefficients and differentiation levels of RUF group and six rice populations including O.nivara(NIV),O.sativa indica(IND),O.sativa aus(AUS),O.sativa temperate japonica(TEJ),O.sativa tropical japonica(TRJ)and O.sativa aromatic(ARO)group.Finally,We discussed the adaptability of RUF at the pressure of natural selection,and then we get these results are as follows:(1)Through the Illumina sequencing technology,we performed SNP analysis on 200 rice genomic data,and obtained 3,264,891 high-quality SNPs loci.Further population genetic analysis showed that 200 accessions of rice seeds could be clearly divided into RUF,NIV,Os-i and Os-j groups.The analysis of the population structure also showed that when K = 4,NIV and RUF groups are separated from each other,and indica and japonica groups are separated from each other.(2)Analysis of population genetics coefficients of different rice resources: LD decay analysis found that the decay rate of wild populations was faster than that of cultivated rice populations,of which O.rufipogon groups decayed fastest and indica rice was slowest;genetic diversity statistics showed that RUF groups has the largest nucleotide diversity,and the overall nucleotide diversity of cultivated rice is lower than that of wild rice;inbreeding coefficient analysis shows that the inbreeding coefficient of wild rice populations is significantly lower than that of cultivated rice populations,of which O.rufipogon gruops is the lowest,which related to the hybrid mating and outcrossingbased breeding systems of RUF,and too high inbreeding coefficients of cultivated rice populations may cause harmful recessive alleles to become pure and produce harmful traits that are not conducive to rice seed survival The level of population differentiation showed that wild rice and cultivated rice populations were significantly separated,among which the O.rufipogon population and the O.sativa temperate japonica and O.sativa indica populations were more differentiated.(3)Continuous pure and regional analysis.The wild rice population has extremely high frequency of short continuous pure and fragments,which indicates that the previous population size of the population was small and there were no recent inbreeding events.There was a high frequency of long continuous in cultivated rice.Pure and fragmentation indicate that its self-crossing frequency is extremely high,and the bottleneck effect has appeared due to the influence of human directional selection.(4)Analysis of the selection signals of O.rufipogon in the natural environment by XP-EHH and Fst selection test methods,a total of 56 potential selection regions were identified,and a total of 357 candidate genes were obtained.The functions of the candidate genes are mainly concentrated In terms of rice yield,plant height,flowering time,energy metabolism,and disease resistance,these genes are most likely related to the adaptation of RUF to biotic and abiotic stress in the natural environment.This study revealed the genetic diversity of O.rufipogon and the adaptation mechanism under natural environment through population genomics data,which not only can provide valuable resources for the cultivation of cultivated rice,but also lay a foundation for further satisfying the rapid and efficient development of the rice planting industry Excellent foundation and theoretical guidance can also deepen the understanding of the genetic basis of O.rufipogon,thereby providing a theoretical basis for effective management and protection of O.rufipogon. |
