Analysis Of Genetic Essence Of Japonica Weedy Rice Based On Genomic Big Data

Weedy rice is a kind of associated weedy rice in cultivated paddy field.It has strong ecological invasiveness,which greatly endangers the yield and quality of cultivation.At the same time,weedy rice has strong adaptability,such as resistance to abiotic stresses such as low temperature,flooding and saline alkali,which provides important gene resources for the genetic improvement of cultivated rice.However,the genetic nature,origin and evolution of weedy rice are not clear,and there are still many disputes in the academic community.At present,there is a consensus that weedy rice is likely to experience multiple origins,and there may be scattered origins of weedy rice in different regions.There are four hypotheses about its evolution:(1)Wild rice gradually evolved into the intermediate transitional form of cultivated rice,that is,the process of semi-domestication;(2)It is produced by the hybridization of wild rice and cultivated rice;(3)It is produced by the separation of characters caused by the hybridization of Indica and Japonica rice with far geographical relationship;(4)It is produced by the "Atavism" of cultivated rice,that is,the process of de-domestication.In order to further explore the genetic essence,origin and evolution of weedy rice,this study carried out genome re-sequencing of Japonica weedy rice sampled at high latitude.Meta analysis was carried out with Japonica rice of different ecotypes in the world in the database.The population genetic structure of natural population composed of weedy rice,wild rice,Japonica cultivated rice and Japonica landrace rice was analyzed;The genetic relationship between weedy rice and different ecotypes of rice was established at the two levels of domestication related genes and genome-wide variations;The genomic regions and candidate genes of "coevolution" and "rejection evolution" of weedy rice and different ecotypes of cultivated rice were further clarified by using genome selection and elimination analysis and machine learning methods,and the accurate discrimination method of weedy rice was established.Finally,through the whole genome association analysis with population niche as phenotype,combined with the above research results,we can deeply understand the genomic essence of weed rice population characteristics.The main results are as follows:(1)The results of phylogeny,population structure analysis and principal component analysis showed that Japonica weedy rice was produced after wild rice was domesticated,and its genetic background was closer to that of Japonica landraced rice,but relatively far from that of Japonica cultivated rice.(2)The haplotype network analysis of domesticated improved genes RC and Wx showed that the ancestral haplotypes were wild rice haplotypes,and then gradually evolved into haplotypes including Japonica weedy rice and Japonica landraced rice,and then evolved into haplotypes including Japonica cultivated rice.Therefore,the Japonica weedy rice population evolved from the wild rice population rather than from the Japonica cultivated rice population.(3)The selection clearance analysis using wild rice population as control found that the genomic selection spectrum of Japonica weedy rice also showed more similar characteristics to that of Japonica landraced rice.Among them,the correlation coefficients of population differentiation index between Japonica weedy rice and Japonica landraced rice,Japonica weedy rice and Japonica cultivated species were 0.91 and 0.70 respectively,and the correlation coefficients of nucleotide diversity ratio were 0.58 and 0.41 respectively.At the same time,candidate genes in the selected region of weedy rice were nominated.(4)Using the machine learning model,by extracting the common characteristics of regional loci among different ecotypes of rice populations,the genomic regions consistent or similar to the characteristics of weedy rice were identified and extracted from different ecotypes of rice from the level of artificial intelligence.It was found that among the 92588 feature windows,25925 windows consistent with the discrimination of cultivated rice and66663 windows consistent with the discrimination of landraced rice.It further shows that the genomic characteristics of weedy rice are closest to those of Japonica landraced rice.At the same time,the feature interval and function obtained by training are also an important reference for realizing the accurate discrimination of weedy rice in the future.(5)The genome-wide association analysis signal with population niche as phenotype overlapped with known domestication improvement genes such as red pericarp gene RC,and also located multiple gene response loci related to the niche of weedy rice.This provides an important reference for revealing the genetic essence of weedy rice all over the world.In conclusion,through the analysis of various types of genomic big data,this study obtained the genomic evidence of "semi-domestication" of Japonica weedy rice,and revealed the genetic feature imprints left by natural selection and competition in the weedy rice genome in the evolution process of accompanying with cultivated rice and environmental adaptation,which provides an important theoretical basis for the further innovation of weedy rice germplasm resources.