Characteristics Evaluation Of Weedy Rice And Analysis Of Its Evolutionary Relationships With Cultivated Rice And Wild Rice

Weedy rice is defined as weedy varieties of cultivated rice infesting paddy fields and negatively influencing rice growth and production.In China,the total area damaged due to weedy rice is more than 3million ha,with crop yield losses can reach to10-20% of gross product.We analyzed 36 pairs of neutral markers,haplotypes from seven genes,and the transcriptome,and conducted a phenotype analysis to elucidate the evolutionary relationships based on 524 rice varieties.Our results indicate a close evolutionary relationship between weedy rice and landrace rice and provided evidence that landrace rice play critical roles in the origin study for weedy rice.The results are as followed:1.Weedy rice clustered with landrace rice,consistent with the phenotypic data for 6 traits PH,CL,HS,PL,SD and PN.The values of PH,CL and PL for weedy rice were slightly lower than landrace rice,but far higher than improved rice.The HS value for weedy rice and landrace rice was similar,but both were lower than that of improved rice.The PN value for weedy rice was much higher than landrace rice and improved rice,while the SD value for weedy rice was much smaller than that of landrace rice and improved rice.Weedy rice and landrace rice have the similar phenotype.2.The clustered result of cold-tolerance phenotype degree showed all varieties were divided three types: cold sensitive type,intermediate type and cold tolerance type.Weedy rice WR19 from Heilongjiang province,Y4 from Liaoning province belong to cold tolerance type;landrace rice Xiaobaigengzi from Heilongjiang province,Hanbaiyi from Jiangsu province belong to cold tolerance type.The clustered result of drought-resistence phenotype degree showed all varieties were divided three types: Drought sensitive type,intermediate type and drought tolerance type,weedy rice WR11 from Heilongjiang province,landrace rice Handao from Jiangsu province belong to drought-resistence type.Therefore,weedy rice from Heilongjiang province have much stronger cold-tolerance and drought-resistence capacity than others.Weedy rice and landrace rice have the similar resistence capacity.3.Population genetic diversity analysis showed the average values of Nei’s index were in the following order: wild rice > weedy rice > landrace rice > improved rice.According to NJ cluster analysis,all samples were divided into three major branches: weedy rice and the majority of landrace rice（Ⅰ）;wild rice and indica rice（Ⅱ）;improved rice and some landrace rice（Ⅲ）.4.Population structure analysis further verified that when K = 2,dividing this population into japonica rice populations P1 and P2（wild rice and indica rice）,and K = 2,P1 population also was divided two poplation: P1-1 and P1-2.When K = 4,P2 population was divided 4 populations: P2-1,P2-2,P2-3 and P2-4.PCA analysis showed all varieties were together into 4 regions,weedy rice and the majority of landrace rice（a）;improved rice and some landrace rice（b）;wild rice solely clustered as an ancient branch population（c）;others varieties cluster a population.5.Haplotype diversity indexes values,nucleotide diversity indexes and population dynamic parameters θω average values were checked,the order of: wild rice > weedy rice > landrace rice > improved rice,Genetic differentiation coefficient values were weedy rice/wild rice > rice/improved rice > weedy rice/landrace rice.Total haplotypes for each gene fragment were: the maximum value is 61 for OsBADH2,and the minmum value 4 for DL.Most major haplotypes were shared by weedy rice,landrace rice and improved rice,but in the DL haplotype,Hap₄ was only found in wild rice,and in Hd1,Hap₉ was only found in weedy rice.Meanwhile,the emergence frequency for some haplotypes had overwhelming proportions in the weedy rice population: Hap₂ in OsBADH2 at 43.75%;Hap₁ in Pita at 90.32%;and Hap₄ in D3 at 45%.Haplotype sequence alignment was performed among whap29,Lhap31 and Chap16,Lhap31 for landrace rice was mutated into the haplotype Chap16 for improved rice through A/G at 617 bp and a G/A mutation at 619 bp,but there was no mutation at 371 bp.In addition,Chap16 for improved rice was mutated into the haplotype whap29 for weedy rice through G/A at 617 bp and a G/A mutation at 371 bp,while whap29 for weedy rice was mutated into Lhap31 for landrace rice through A/G at 619 bp and an A/G mutation at 371 bp.Therefore,weedy rice may be a dynamic state or intermediate in the evolution from improved rice to weedy rice to landrace rice,providing an explanation or clue to the origin of weedy rice.SNPs play important roles in progress of weedy rice evolution.6.Comparative analysis of the OsSPY gene sequence showed an 18 bp InDel was found in the sequences of weedy rice and landrace rice from HLJ,JL,LN and NX compared with the Nipponbare OsSPY gene sequence.However,the 18 bp fragment was rare in weedy rice and landrace rice from JS and Korea.InDels play important roles in progress of weedy rice evolution.7.Basing on comparative transcriptome analysis from 15 samples（5 samples for weedy rice,5 samples for landrace rice,5 samples for improved rice）,we chosed three samples（WR21,MDL and JD106）,then we analyzed shared SNPs and InDels between WR21 and MDL,WR21 and JD106,MDL and JD106.More common SNPs and InDels were identified between WR21 and MDL.Shared SNPs were mainly distributed on chromosomes 1,2,4,6,7 and 8.On 4 Chromosome,the maxmum shared SNPs were checked,A/G and T/C are the primary variation formation.In a word,weedy rice and landrace rice have been similar on phenotype,resistence,genetic diversity,haplotype evolution selection,variation region and gene expression pattern,therefore,the more closer revolution relationship exist between weedy rice and landrace rice,which provided new clues to the origin of weedy rice.