Exploring The Origin Of Weedy Rice Using Four Domestication Genes

Cultivated rice(Oryza sativa L.)is the earliest domestication crop in the world,andit's the main food for more than one-third of the population in the world currently.Cultivated rice was domesticated about 8000 years ago,and there are many variation phenotypic traits.Such as,pericarp color,apiculus coloration,shattering,dormancy and flowering time.This variation is result from the mutation of domestication gene that control corresponding phenotypic traits.So,the domestication gene play an important role to the phenotypic traits variation.Weedy rice is a conspecific form of cultivated rice(Oryza sativa L.)that infests rice fields,and share the phenotypic traits with cultivated rice,then compete limit space and nutrition resources with Cultivated rice.Therefore,it is really difficult to control the weedy rice in rice field.Hence,weedy rice results to severe crop losses in the world rice industry region.However,until now we don't know the origin of weedy clearly in the different world region.With the development of Molecular biology,more and more domestication gene was cloned,Therefore,it's provide a new method to researching the origin of weedy rice.Rc gene is the key gene that control rice pericarp color.rc has a 14 bp deletion in exon 7 leading Rc loss of function,then the synthesis of anthocyanins was terminated and rice pericarp color turn in to white.Nonfunctional rc alleles were strongly favored during rice domestication,and 97%cultivated varieties have nonpigmented pericarps.DTH7 is the most important gene in flowering time path way.The mutation of this gene(the 8 bp/2 bp frameshift and the variation T to C in DTH 7 gene result translation stop in advance)has an important affect on the variation of rice flowering time.OsC1 is the key regulate factor of apiculus coloration.The different mutation of OsCl is responsible for different apiculus coloration.There are two frameshift deletion in the third exon of OsC1 gene-which lead to OsC1 gene loss of function,then the apiculus turn to white.ALS gene is associate with the rice herbicide resistance.The variation of weedy rice ALS has an important effect on the herbicide resistance of weedy rice,which has serious restrict to Clearfield rice in long time.In order to explore where is the weedy rice derivate,we sequenced four domestication gene Rc,DTH7,OsC1,ALS and around region of cultivated rice,wild rice and weedy rice by Target Sequence,then we perform the Sequence alignment,construct ML tree,making genetic variation and genetic diversity analysis fistly.Next,in order to identify functional Rc alleles confer particular fitness benefits in weedy rice populations,we also compare the Rc allelic distributions with other rice domestication genes sh4,Bh4,An-1.Via our study,we got several conclusion as follow:1.US weedy rice is mainly origin from domestication rice aus/indica,and US cultivated rice japonica also contribute to the evolution of US weedy rice;Domestication rice aus/indica and wild rice O.rufipogon contribute to the formation of Malaysian weedy rice together;The Origin of Souther Asian weedy is most complex,domestication rice aus/indica,US cultivated rice japonica and wild rice O.rufipogon is three key factor for Souther Asian weedy rice quickly spreading.2.The genetic diversity of US weedy rice is relatively lower.It's mean the genetic diversity of US weedy rice is affected by Genetic bottleneck during rice domestication history.3.Comparison of Rc allelic distributions with other rice domestication genes suggests that functional Rc alleles may confer particular fitness benefits in weedy rice populations,for example,by conferring seed dormancy.This may promote functional Rc introgression from local wild Oryza populations.In additaion,we also found white Malaysian weedy rice that is derivate from white cultivated rice japonica have 13 SNPs compare with red Malaysian weedy rice that derivate from red landrace aus/indica in Rc gene.4.By calculating the flowering time phenotype trait of US weedy rice,we found that the US weedy rice SH flowering time is early than US weedy rice BHA.After DTH7 gene sequence analysis,we found there is a 8 bp deletion frameshift deletion which result amino acid translation termination in advance in US weedy rice SH.We also found the 8 bp deletion in US weedy rice ancestor indica,but the flowering time of US weedy rice ancestor indica is not consistent with US weedy rice SH.This mean that single gene mutation can not explain the variation of rice flowering time.5.The reason for lower genetic diversity of US weedy rice and Malaysian weedy rice at OsCl allele is gene introgression from indica OsCl allele in to weedy rice.Hence,Malaysian weedy rice and US weedy rice was not selected.6.There is a 10 bp frameshift deletion in OsC1 gene for all white apiculus coloration weedy rice.7.All Malaysian weedy rice,US weedy rice and Souther Asian weedy rice have herbicide resistance,and the herbicide resistance is between 80%-90%.The herbicide resistance of weedy rice is closely related to point mutations on ALS genes.We have identified nine amino acid mutation on herbicide resistance weedy rice.And 5 of them are accompany by the changes of polarity and chargeability(A 11T,P67T,A122T,W293T,E604D).And the three mutations(P67T,W293R,E609D)located in the ?,?,? region of ALS enzyme respectively.Among of them:(1)There are 51 Malaysian weedy rice have A11T replacement.All US weedy rice arise A11T replacement.32 Souther Asian weedy rice arise A11T replacement.(2)There are 14 Malaysian weedy rice arise P67T replacement.However,we are not found P67T replacement in all US weedy rice.In addition,there are 17 Souther Asian weedy rice arise P67T replacement.(3)All US weedy rice,Malaysian weedy rice and Souther Asian weedy rice has W239T replacement in ALS enzyme.(4)There are 30 Malaysian weedy rice arise E604D replacement,and there are 6 South Asian weedy rice also arise E604 replacement.However,we are not found E604D replacement in US weedy rice.8.As we all know,A122T replacement is arise in Clearfield rice firstly.With the popularization and the rapid development of Clearfield rice,we also found A122T replacement in most of Malaysian weedy rice,South Asian weedy rice and US weedy rice respectively.We found there is 42 Malaysian weedy rice have A122T replacement among 52 Malaysian weedy rice.There is 26 Souther Asian weedy rice have A122T replacement among 35 Souther Asian weedy rice.In addition,there are 47 US weedy rice rise A122T replacement among 51 US weedy rice in our sample sets.This mean gene flow between Clearfield rice and weedy also play an important role to the quickly spreading of herbicide resistance weedy rice in the world region.